From 1db7080bd66407fabab154f3d5bcd31949a12fb4 Mon Sep 17 00:00:00 2001
From: Edward Misback <misback@cs.washington.edu>
Date: Tue, 24 Mar 2026 07:28:23 -0400
Subject: [PATCH 01/22] Image resize, separate experimental tools from
 standard.

---
 .../webview-ui/src/additionalTools.tsx        | 2307 ++++++++++++++
 vscode-extension/webview-ui/src/tools.tsx     | 2697 ++---------------
 2 files changed, 2562 insertions(+), 2442 deletions(-)
 create mode 100644 vscode-extension/webview-ui/src/additionalTools.tsx

diff --git a/vscode-extension/webview-ui/src/additionalTools.tsx b/vscode-extension/webview-ui/src/additionalTools.tsx
new file mode 100644
index 0000000..893798e
--- /dev/null
+++ b/vscode-extension/webview-ui/src/additionalTools.tsx
@@ -0,0 +1,2307 @@
+import { AnnotationEditorProps } from "./App";
+import React, { useEffect, useState, useRef } from "react";
+import { ObjectInspector } from "react-inspector";
+import { ChatMessage, lmApi, mockLmApi } from "./lm-api-client";
+import { vscode } from "./utilities/vscode";
+
+const commonTextStyle: React.CSSProperties = {
+  fontFamily: "Poppins, sans-serif",
+  fontSize: "14px",
+  color: "black",
+};
+
+// dead code
+const RunCodeSegment: React.FC<AnnotationEditorProps> = (props) => {
+  const [apiResName, setApiResName] = useState<string>(props.value.metadata.apiResName || "");
+  const [apiRes, setApiRes] = useState<string>(props.value.metadata.apiRes || "");
+  const [code, setCode] = useState<string[]>(props.value.metadata.code || ["", "", ""]);
+  const [pinBody, setPinBody] = useState<boolean>(props.value.metadata.pinBody || false);
+  const [showHead, setShowHead] = useState<boolean>(props.value.metadata.showHead || false);
+  const [showTail, setShowTail] = useState<boolean>(props.value.metadata.showTail || false);
+
+  function addReturn(code: string): string {
+    const lines = code.trim().split("\n");
+    if (lines.length === 0) {
+      return "";
+    }
+    const lastLine = lines[lines.length - 1];
+    lines[lines.length - 1] = `return ${lastLine.trim()}`;
+    return lines.join("\n");
+  }
+
+  async function runAndUpdateCode(): Promise<void> {
+    try {
+      let empty = true;
+      for (let i = 0; i < code.length; i++) {
+        if (String(code[i]).trim() !== "") {
+          empty = false;
+          break;
+        }
+      }
+      if (apiRes !== "" && apiResName === "") {
+        empty = false;
+      }
+      if (empty) {
+        props.utils.setMetadata({
+          error: "No code to run",
+          response: undefined,
+          code: code,
+        });
+        return;
+      }
+
+      let joinedCode = code.join("\n");
+      if (apiRes !== "" && apiResName !== "") {
+        joinedCode = `const ${apiResName} = Promise.resolve(${apiRes});\n${joinedCode}`;
+      }
+
+      const asyncFunction = new Function(`return (async () => { ${joinedCode} })();`);
+      let result = await asyncFunction();
+
+      if (result === undefined) {
+        const newCode = addReturn(joinedCode);
+        try {
+          const asyncReturnFunction = new Function(`return (async () => { ${newCode} })();`);
+          result = await asyncReturnFunction();
+        } catch {}
+      }
+
+      props.utils.setMetadata({
+        response: result || "Undefined",
+        error: undefined,
+        code,
+        apiRes,
+        apiResName,
+      });
+    } catch (e) {
+      props.utils.setMetadata({
+        response: undefined,
+        error: e instanceof Error ? e.message : String(e),
+        code,
+        apiRes,
+        apiResName,
+      });
+    }
+  }
+
+  return (
+    <div style={{ marginBottom: "10px" }}>
+      <div style={{ marginBottom: "10px" }}>
+        <label style={commonTextStyle}>
+          <strong>Cached API Response</strong>
+        </label>
+        <div style={{ marginBottom: "10px" }}>
+          <label style={commonTextStyle}>Mock Response:</label>
+          <br></br>
+          <textarea
+            rows={4}
+            value={apiRes}
+            placeholder="Enter a JavaScript object..."
+            onChange={(e) => setApiRes(e.target.value)}
+            style={{
+              ...commonTextStyle,
+              width: "-webkit-fill-available",
+              padding: "5px",
+              border: "1px solid #ccc",
+              borderRadius: "4px",
+            }}
+          />
+        </div>
+        <div style={{ marginBottom: "10px" }}>
+          <label style={commonTextStyle}>Mock Response Variable Name:</label>
+          <br />
+          <input
+            value={apiResName}
+            placeholder="Enter a variable name..."
+            onChange={(e) => setApiResName(e.target.value)}
+            style={{
+              ...commonTextStyle,
+              marginBottom: "10px",
+              width: "-webkit-fill-available",
+              padding: "5px",
+              border: "1px solid #ccc",
+              borderRadius: "4px",
+            }}
+          />
+        </div>
+        <div style={{ marginBottom: "10px" }}>
+          <label style={commonTextStyle}>Head:</label>
+          <br></br>
+          <textarea
+            rows={4}
+            value={code[0]}
+            placeholder="Enter other JS preprocessing code..."
+            onChange={(e) => {
+              const newCode = [...code];
+              newCode[0] = e.target.value;
+              setCode(newCode);
+            }}
+            style={{
+              ...commonTextStyle,
+              width: "-webkit-fill-available",
+              marginBottom: "10px",
+              padding: "5px",
+              border: "1px solid #ccc",
+              borderRadius: "4px",
+            }}
+          />
+        </div>
+        <div style={{ marginBottom: "10px" }}>
+          <label style={commonTextStyle}>Body:</label>
+          <br></br>
+          <textarea
+            rows={4}
+            placeholder="Enter a JavaScript expression..."
+            value={pinBody ? props.utils.getText() : code[1]}
+            onChange={(e) => {
+              if (!pinBody) {
+                const newCode = [...code];
+                newCode[1] = e.target.value;
+                setCode(newCode);
+              }
+            }}
+            style={{
+              ...commonTextStyle,
+              width: "-webkit-fill-available",
+              padding: "5px",
+              border: "1px solid #ccc",
+              borderRadius: "4px",
+            }}
+          />
+          <div>
+            <label style={commonTextStyle}>
+              <input
+                type="checkbox"
+                checked={pinBody}
+                onChange={() => {
+                  setPinBody(!pinBody);
+                  props.utils.setMetadata({ pinBody: !pinBody });
+                }}
+              />
+              Pin body to annotated document text
+            </label>
+          </div>
+        </div>
+        <div style={{ marginBottom: "10px" }}>
+          <label style={commonTextStyle}>Tail:</label>
+          <br></br>
+          <textarea
+            rows={4}
+            placeholder="Enter other JS postprocessing code..."
+            value={code[2]}
+            onChange={(e) => {
+              const newCode = [...code];
+              newCode[2] = e.target.value;
+              setCode(newCode);
+            }}
+            style={{
+              ...commonTextStyle,
+              width: "-webkit-fill-available",
+              marginBottom: "10px",
+              padding: "5px",
+              border: "1px solid #ccc",
+              borderRadius: "4px",
+            }}
+          />
+        </div>
+      </div>
+      {props.value.metadata.error && (
+        <div style={{ color: "red", marginBottom: "10px", ...commonTextStyle }}>
+          An error occurred: {props.value.metadata.error}
+        </div>
+      )}
+      {props.value.metadata.response && (
+        <div style={{ marginBottom: "10px", ...commonTextStyle }}>
+          <strong>Response:</strong> <ObjectInspector data={props.value.metadata.response} />
+        </div>
+      )}
+      <div style={{ marginBottom: "10px" }}>
+        <button
+          onClick={runAndUpdateCode}
+          style={{
+            marginRight: "10px",
+            ...commonTextStyle,
+            padding: "5px 10px",
+            border: "1px solid #ccc",
+            borderRadius: "4px",
+            cursor: "pointer",
+          }}>
+          Run Code
+        </button>
+        {props.value.metadata.response && (
+          <button
+            onClick={() =>
+              props.utils.setMetadata({
+                response: undefined,
+                error: undefined,
+              })
+            }
+            style={{
+              ...commonTextStyle,
+              padding: "5px 10px",
+              border: "1px solid #ccc",
+              borderRadius: "4px",
+              cursor: "pointer",
+            }}>
+            Clear Output
+          </button>
+        )}
+      </div>
+    </div>
+  );
+};
+
+const ExplainInEnglish: React.FC<AnnotationEditorProps> = (props) => {
+  // State management for explanations
+  const [explanations, setExplanations] = useState({
+    what: props.value.metadata.whatExplanation || "",
+    how: props.value.metadata.howExplanation || "",
+    context: props.value.metadata.contextExplanation || "",
+    why: props.value.metadata.whyExplanation || "",
+  });
+
+  const [presentationSummary, setPresentationSummary] = useState(
+    props.value.metadata.presentationSummary || ""
+  );
+
+  const [explanationMode, setExplanationMode] = useState<"presentation" | "in-depth">(
+    props.value.metadata.explanationMode || "presentation"
+  );
+
+  const [isLoading, setIsLoading] = useState(false);
+  const [error, setError] = useState<string | null>(null);
+  const [executionResult, setExecutionResult] = useState<string | null>(
+    props.value.metadata.executionResult || null
+  );
+  const [executionError, setExecutionError] = useState<string | null>(
+    props.value.metadata.executionError || null
+  );
+  const [useMock, setUseMock] = useState(false);
+  const [isExecuting, setIsExecuting] = useState(false);
+
+  // Track if component is mounted
+  const isMounted = useRef(true);
+
+  useEffect(() => {
+    return () => {
+      isMounted.current = false;
+    };
+  }, []);
+
+  // Get the highlighted code and document context
+  const highlightedCode = props.utils.getText();
+  const documentText = props.value.document || "";
+  const startPos = props.value.start;
+  const endPos = props.value.end;
+
+  // Save state changes to metadata
+  useEffect(() => {
+    props.utils.setMetadata({
+      whatExplanation: explanations.what,
+      howExplanation: explanations.how,
+      contextExplanation: explanations.context,
+      whyExplanation: explanations.why,
+      presentationSummary,
+      explanationMode,
+      executionResult,
+      executionError,
+    });
+  }, [explanations, presentationSummary, explanationMode, executionResult, executionError]);
+
+  // Create formatted document with highlighted section
+  const createFormattedDocument = () => {
+    if (!documentText) {
+      return "";
+    }
+
+    const before = documentText.substring(0, startPos);
+    const highlighted = documentText.substring(startPos, endPos);
+    const after = documentText.substring(endPos);
+
+    return `${before}<<<HIGHLIGHTED>${highlighted}</HIGHLIGHTED>>>${after}`;
+  };
+
+  // Generate English explanation
+  const generateExplanation = async () => {
+    if (!highlightedCode.trim()) {
+      setError("No code selected to explain");
+      return;
+    }
+
+    setIsLoading(true);
+    setError(null);
+
+    try {
+      const formattedDocument = createFormattedDocument();
+
+      const basePrompt = `You are a helpful assistant that explains JavaScript code in simple, clear English. 
+
+    You will be given a document with a highlighted section marked by <<<HIGHLIGHTED>...</HIGHLIGHTED>>> tags.
+
+    Please provide explanations for the highlighted code in four specific categories:
+
+    1. WHAT: What does this code do? (describe the main functionality and purpose)
+    2. HOW: How does this code work? (explain the technical implementation and logic flow)
+    3. CONTEXT: What is this code's function in the context of the entire class/component it belongs to? (explain its role in the larger system)
+    4. WHY: Why is this code needed? (explain the problem it solves and its importance)
+
+    Use clear, non-technical language that a beginner could understand. Focus on being concise but comprehensive.`;
+
+      if (explanationMode === "presentation") {
+        const presentationPrompt: ChatMessage[] = [
+          {
+            role: "system",
+            content: `${basePrompt}
+
+    Format your response as a single cohesive explanation with bullet points for each category:
+
+    **What the code does:**
+    • [2-3 concise bullet points]
+
+    **How the code works:**
+    • [2-3 concise bullet points]
+
+    **Context within the class/component:**
+    • [2-3 concise bullet points]
+
+    **Why it's needed:**
+    • [2-3 concise bullet points]
+
+    Keep each bullet point to 1-2 sentences maximum. This should be easy to read without scrolling.`,
+          },
+          {
+            role: "user",
+            content:
+              `Here is the code with the highlighted section:\n\n${
+                formattedDocument || highlightedCode
+              }\n\n` + `Please explain the highlighted code in presentation format.`,
+          },
+        ];
+
+        let response: string;
+        if (useMock) {
+          await new Promise((resolve) => setTimeout(resolve, 1000));
+          response = `**What the code does:**
+    • Sets up state variables for managing user interface interactions
+    • Handles data processing and validation logic
+    • Manages component lifecycle and cleanup operations
+
+    **How the code works:**
+    • Uses React hooks to track component state changes
+    • Implements async functions for API communication
+    • Applies error handling with try-catch blocks
+
+    **Context within the class/component:**
+    • Serves as the core data processing logic for the component
+    • Integrates with other component methods for state management
+    • Provides essential functionality for user interactions
+
+    **Why it's needed:**
+    • Ensures proper data flow and state consistency
+    • Prevents memory leaks and handles edge cases
+    • Enables responsive user experience and error recovery`;
+        } else {
+          try {
+            response = await lmApi.chat(presentationPrompt, {
+              vendor: "copilot",
+              family: "gpt-4o",
+              temperature: 0.7,
+            });
+          } catch (apiError) {
+            console.log("API call failed, falling back to mock:", apiError);
+            response = `**What the code does:**
+    • Sets up state variables for managing user interface interactions
+    • Handles data processing and validation logic
+    • Manages component lifecycle and cleanup operations
+
+    **How the code works:**
+    • Uses React hooks to track component state changes
+    • Implements async functions for API communication
+    • Applies error handling with try-catch blocks
+
+    **Context within the class/component:**
+    • Serves as the core data processing logic for the component
+    • Integrates with other component methods for state management
+    • Provides essential functionality for user interactions
+
+    **Why it's needed:**
+    • Ensures proper data flow and state consistency
+    • Prevents memory leaks and handles edge cases
+    • Enables responsive user experience and error recovery`;
+          }
+        }
+
+        if (isMounted.current) {
+          setPresentationSummary(response);
+        }
+      } else {
+        // In-depth mode - get detailed explanations for each category
+        const inDepthPrompt: ChatMessage[] = [
+          {
+            role: "system",
+            content: `${basePrompt}
+
+    You MUST respond with ONLY a valid JSON object. No additional text, explanations, or formatting outside the JSON.
+
+    The JSON should have exactly this structure:
+    {
+      "what": "Detailed explanation of what the code does (3-5 sentences)...",
+      "how": "Detailed explanation of how it works technically (3-5 sentences)...",
+      "context": "Detailed explanation of its role in the larger system (3-5 sentences)...",
+      "why": "Detailed explanation of why it's necessary (3-5 sentences)..."
+    }
+
+    Each value should be a single string with 3-5 sentences. Do not include any markdown, formatting, or line breaks within the strings.`,
+          },
+          {
+            role: "user",
+            content:
+              `Here is the code with the highlighted section:\n\n${
+                formattedDocument || highlightedCode
+              }\n\n` + `Please provide detailed explanations for each category in JSON format.`,
+          },
+        ];
+
+        let response: string;
+        if (useMock) {
+          await new Promise((resolve) => setTimeout(resolve, 1000));
+          response = JSON.stringify({
+            what: "This code defines state management and UI interaction logic for a React component. It establishes multiple state variables using the useState hook to track different aspects of the component's behavior, including user inputs, loading states, error conditions, and execution results. The code also sets up effect hooks to handle component lifecycle events and data persistence.\n\nThe primary function is to create a controlled interface that responds to user actions while maintaining data integrity. It manages both the visual presentation of information and the underlying data processing that supports the component's functionality.\n\nAdditionally, this code implements proper cleanup mechanisms to prevent memory leaks and ensures that asynchronous operations are handled correctly even when the component unmounts during execution.",
+            how: "The implementation uses React's built-in hooks pattern to manage state and side effects. The useState hooks create reactive state variables that automatically trigger re-renders when their values change. Each state variable serves a specific purpose and is updated through setter functions that maintain immutability principles.\n\nThe useEffect hooks create a dependency tracking system that automatically runs cleanup or update logic when specific values change. This creates a reactive programming model where changes in one part of the system automatically propagate to other dependent parts.\n\nThe code also implements proper error boundary patterns using try-catch blocks and loading states, ensuring that the user interface remains responsive and informative even when operations fail or take time to complete.",
+            context:
+              "Within the larger component architecture, this code serves as the foundational state management layer that all other component methods depend on. It acts as the single source of truth for the component's current status and provides the reactive infrastructure that other functions can interact with.\n\nThis state management setup enables other parts of the component to perform operations like API calls, user input handling, and data validation while maintaining consistent state across the entire component lifecycle. It integrates with the component's rendering logic to ensure that UI changes reflect the current application state.\n\nThe code also establishes the communication patterns between this component and its parent components or global state management systems, ensuring that data flows correctly throughout the application hierarchy.",
+            why: "This state management structure is essential for creating a reliable and user-friendly interface. Without proper state tracking, the component would not be able to provide visual feedback to users about loading states, errors, or successful operations, leading to a poor user experience.\n\nThe structured approach to state management prevents common React pitfalls like state inconsistencies, memory leaks from unmounted components, and race conditions from asynchronous operations. This defensive programming approach ensures the component remains stable even under adverse conditions.\n\nFurthermore, this pattern establishes a maintainable codebase where future developers can easily understand and modify the component's behavior. The clear separation of concerns and consistent naming conventions make the code self-documenting and reduce the likelihood of bugs during maintenance or feature additions.",
+          });
+        } else {
+          try {
+            response = await lmApi.chat(inDepthPrompt, {
+              vendor: "copilot",
+              family: "gpt-4o",
+              temperature: 0.7,
+            });
+          } catch (apiError) {
+            console.log("API call failed, falling back to mock:", apiError);
+            response = JSON.stringify({
+              what: "This code defines state management and UI interaction logic for a React component. It establishes multiple state variables using the useState hook to track different aspects of the component's behavior, including user inputs, loading states, error conditions, and execution results. The code also sets up effect hooks to handle component lifecycle events and data persistence.",
+              how: "The implementation uses React's built-in hooks pattern to manage state and side effects. The useState hooks create reactive state variables that automatically trigger re-renders when their values change. Each state variable serves a specific purpose and is updated through setter functions that maintain immutability principles.",
+              context:
+                "Within the larger component architecture, this code serves as the foundational state management layer that all other component methods depend on. It acts as the single source of truth for the component's current status and provides the reactive infrastructure that other functions can interact with.",
+              why: "This state management structure is essential for creating a reliable and user-friendly interface. Without proper state tracking, the component would not be able to provide visual feedback to users about loading states, errors, or successful operations, leading to a poor user experience.",
+            });
+          }
+        }
+
+        try {
+          // Try to parse as JSON first
+          const parsedResponse = JSON.parse(response);
+          if (isMounted.current) {
+            setExplanations({
+              what: parsedResponse.what || "",
+              how: parsedResponse.how || "",
+              context: parsedResponse.context || "",
+              why: parsedResponse.why || "",
+            });
+          }
+        } catch (parseError) {
+          // If JSON parsing fails, try to extract content between JSON markers or use fallback
+          console.log("JSON parsing failed, attempting to extract or use fallback:", parseError);
+
+          try {
+            // Try to find JSON content within the response
+            const jsonMatch = response.match(/\{[\s\S]*\}/);
+            if (jsonMatch) {
+              const parsedResponse = JSON.parse(jsonMatch[0]);
+              if (isMounted.current) {
+                setExplanations({
+                  what: parsedResponse.what || "",
+                  how: parsedResponse.how || "",
+                  context: parsedResponse.context || "",
+                  why: parsedResponse.why || "",
+                });
+              }
+            } else {
+              // Fallback: treat the response as a single explanation and distribute it
+              const fallbackText = response.trim();
+              const sections = fallbackText.split(/(?:\n\s*){2,}/); // Split on double line breaks
+
+              if (isMounted.current) {
+                setExplanations({
+                  what: sections[0] || fallbackText,
+                  how: sections[1] || "Technical implementation details for the highlighted code.",
+                  context:
+                    sections[2] ||
+                    "This code functions as part of the larger component/class structure.",
+                  why:
+                    sections[3] ||
+                    "This code is necessary to ensure proper functionality and user experience.",
+                });
+              }
+            }
+          } catch (secondParseError) {
+            console.log("All parsing attempts failed, using basic fallback");
+            if (isMounted.current) {
+              setExplanations({
+                what: response || "Unable to generate explanation",
+                how: "Technical implementation could not be parsed from the response.",
+                context: "Context information could not be extracted.",
+                why: "Reasoning could not be determined from the response.",
+              });
+            }
+          }
+        }
+      }
+    } catch (err) {
+      const errorMsg =
+        err instanceof Error ? err.message : "An error occurred while generating explanation";
+
+      if (isMounted.current) {
+        setError(errorMsg);
+      }
+    } finally {
+      if (isMounted.current) {
+        setIsLoading(false);
+      }
+    }
+  };
+
+  // Execute the highlighted code (keeping original logic)
+  const executeCode = async () => {
+    setIsExecuting(true);
+    setExecutionError(null);
+    setExecutionResult(null);
+
+    try {
+      const code = highlightedCode.trim();
+      let result;
+
+      try {
+        const asyncFunction = new Function(`
+              'use strict';
+              return (async () => {
+                ${code}
+              })();
+            `);
+        result = await asyncFunction();
+      } catch (firstError) {
+        const lines = code.split("\n");
+        if (lines.length > 0) {
+          const lastLine = lines[lines.length - 1].trim();
+          if (!lastLine.startsWith("return") && !lastLine.startsWith("throw")) {
+            lines[lines.length - 1] = `return ${lastLine}`;
+            const modifiedCode = lines.join("\n");
+
+            try {
+              const asyncFunction = new Function(`
+                    'use strict';
+                    return (async () => {
+                      ${modifiedCode}
+                    })();
+                  `);
+              result = await asyncFunction();
+            } catch (secondError) {
+              throw firstError;
+            }
+          } else {
+            throw firstError;
+          }
+        } else {
+          throw firstError;
+        }
+      }
+
+      if (result === undefined) {
+        setExecutionResult("undefined");
+      } else if (result === null) {
+        setExecutionResult("null");
+      } else if (typeof result === "object") {
+        setExecutionResult(JSON.stringify(result, null, 2));
+      } else {
+        setExecutionResult(String(result));
+      }
+    } catch (err) {
+      setExecutionError(err instanceof Error ? err.message : String(err));
+    } finally {
+      setIsExecuting(false);
+    }
+  };
+
+  return (
+    <div
+      style={{
+        padding: "12px",
+        fontFamily: "Poppins, -apple-system, BlinkMacSystemFont, sans-serif",
+        fontSize: "14px",
+        maxWidth: "100%",
+      }}>
+      <div style={{ marginBottom: "16px" }}>
+        <h3
+          style={{
+            margin: "0 0 12px 0",
+            fontSize: "16px",
+            fontWeight: "600",
+            color: "#333",
+          }}>
+          Code Explanation in Plain English
+        </h3>
+
+        <div
+          style={{
+            display: "flex",
+            gap: "10px",
+            alignItems: "center",
+            marginBottom: "12px",
+            flexWrap: "wrap",
+          }}>
+          <button
+            onClick={generateExplanation}
+            disabled={isLoading}
+            style={{
+              padding: "8px 16px",
+              backgroundColor: isLoading ? "#e0e0e0" : "#0078D4",
+              color: "white",
+              border: "none",
+              borderRadius: "4px",
+              cursor: isLoading ? "not-allowed" : "pointer",
+              fontSize: "14px",
+              fontWeight: "500",
+              transition: "background-color 0.2s",
+            }}>
+            {isLoading ? "Generating..." : "Generate Explanation"}
+          </button>
+
+          <div style={{ display: "flex", alignItems: "center", gap: "8px" }}>
+            <label style={{ fontSize: "13px", color: "#666", fontWeight: "500" }}>Mode:</label>
+            <select
+              value={explanationMode}
+              onChange={(e) => setExplanationMode(e.target.value as "presentation" | "in-depth")}
+              style={{
+                padding: "6px 10px",
+                borderRadius: "4px",
+                border: "1px solid #ccc",
+                fontSize: "13px",
+                backgroundColor: "white",
+              }}>
+              <option value="presentation">Presentation (Summary)</option>
+              <option value="in-depth">In-Depth (Detailed)</option>
+            </select>
+          </div>
+
+          <label
+            style={{
+              display: "flex",
+              alignItems: "center",
+              fontSize: "13px",
+              cursor: "pointer",
+              color: "#666",
+            }}>
+            <input
+              type="checkbox"
+              checked={useMock}
+              onChange={() => setUseMock(!useMock)}
+              style={{ marginRight: "6px" }}
+            />
+            Use mock API
+          </label>
+        </div>
+
+        {error && (
+          <div
+            style={{
+              color: "#D83B01",
+              backgroundColor: "#FFF4F2",
+              padding: "10px",
+              borderRadius: "4px",
+              marginBottom: "12px",
+              fontSize: "13px",
+              border: "1px solid #FDBCB4",
+            }}>
+            ⚠️ {error}
+          </div>
+        )}
+
+        {explanationMode === "presentation" ? (
+          <div style={{ marginBottom: "16px" }}>
+            <label
+              style={{
+                display: "block",
+                marginBottom: "8px",
+                fontWeight: "600",
+                fontSize: "14px",
+                color: "#444",
+              }}>
+              Code Explanation Summary:
+            </label>
+            <textarea
+              value={presentationSummary}
+              onChange={(e) => setPresentationSummary(e.target.value)}
+              placeholder="Click 'Generate Explanation' to get a concise summary with bullet points for What, How, Context, and Why..."
+              style={{
+                width: "100%",
+                minHeight: "200px",
+                padding: "12px",
+                borderRadius: "4px",
+                border: "1px solid #ccc",
+                fontSize: "14px",
+                lineHeight: "1.6",
+                resize: "vertical",
+                fontFamily: "inherit",
+                backgroundColor: "#FAFAFA",
+              }}
+            />
+          </div>
+        ) : (
+          <div style={{ marginBottom: "16px" }}>
+            {[
+              { key: "what", title: "What does this code do?", color: "#E3F2FD" },
+              { key: "how", title: "How does this code work?", color: "#F3E5F5" },
+              { key: "context", title: "Context within the class/component", color: "#E8F5E8" },
+              { key: "why", title: "Why is this code needed?", color: "#FFF3E0" },
+            ].map(({ key, title, color }) => (
+              <div key={key} style={{ marginBottom: "16px" }}>
+                <label
+                  style={{
+                    display: "block",
+                    marginBottom: "8px",
+                    fontWeight: "600",
+                    fontSize: "14px",
+                    color: "#444",
+                  }}>
+                  {title}
+                </label>
+                <textarea
+                  value={explanations[key as keyof typeof explanations]}
+                  onChange={(e) => setExplanations((prev) => ({ ...prev, [key]: e.target.value }))}
+                  placeholder={`Detailed explanation of ${key}...`}
+                  style={{
+                    width: "100%",
+                    minHeight: "120px",
+                    padding: "12px",
+                    borderRadius: "4px",
+                    border: "1px solid #ccc",
+                    fontSize: "14px",
+                    lineHeight: "1.6",
+                    resize: "vertical",
+                    fontFamily: "inherit",
+                    backgroundColor: color,
+                  }}
+                />
+              </div>
+            ))}
+          </div>
+        )}
+
+        <div
+          style={{
+            borderTop: "1px solid #E1E1E1",
+            paddingTop: "16px",
+            marginTop: "16px",
+          }}>
+          <h4
+            style={{
+              margin: "0 0 12px 0",
+              fontSize: "15px",
+              fontWeight: "600",
+              color: "#333",
+            }}>
+            Code Execution
+          </h4>
+
+          <button
+            onClick={executeCode}
+            disabled={isExecuting || !highlightedCode.trim()}
+            style={{
+              padding: "8px 16px",
+              backgroundColor: isExecuting ? "#e0e0e0" : "#107C10",
+              color: "white",
+              border: "none",
+              borderRadius: "4px",
+              cursor: isExecuting || !highlightedCode.trim() ? "not-allowed" : "pointer",
+              fontSize: "14px",
+              fontWeight: "500",
+              marginBottom: "12px",
+              transition: "background-color 0.2s",
+            }}>
+            {isExecuting ? "Executing..." : "▶ Execute Code"}
+          </button>
+
+          {executionResult !== null && (
+            <div
+              style={{
+                backgroundColor: "#F0FFF4",
+                border: "1px solid #B7EB8F",
+                borderRadius: "4px",
+                padding: "12px",
+                marginTop: "12px",
+              }}>
+              <div
+                style={{
+                  fontWeight: "600",
+                  marginBottom: "8px",
+                  color: "#52C41A",
+                  fontSize: "13px",
+                }}>
+                ✓ Execution Result:
+              </div>
+              <pre
+                style={{
+                  margin: 0,
+                  fontFamily: "Consolas, Monaco, 'Courier New', monospace",
+                  fontSize: "13px",
+                  whiteSpace: "pre-wrap",
+                  wordBreak: "break-word",
+                  color: "#333",
+                  backgroundColor: "white",
+                  padding: "8px",
+                  borderRadius: "3px",
+                }}>
+                {executionResult}
+              </pre>
+            </div>
+          )}
+
+          {executionError && (
+            <div
+              style={{
+                backgroundColor: "#FFF2F0",
+                border: "1px solid #FFCCC7",
+                borderRadius: "4px",
+                padding: "12px",
+                marginTop: "12px",
+              }}>
+              <div
+                style={{
+                  fontWeight: "600",
+                  marginBottom: "8px",
+                  color: "#FF4D4F",
+                  fontSize: "13px",
+                }}>
+                ✗ Execution Error:
+              </div>
+              <pre
+                style={{
+                  margin: 0,
+                  fontFamily: "Consolas, Monaco, 'Courier New', monospace",
+                  fontSize: "13px",
+                  whiteSpace: "pre-wrap",
+                  wordBreak: "break-word",
+                  color: "#8B0000",
+                  backgroundColor: "white",
+                  padding: "8px",
+                  borderRadius: "3px",
+                }}>
+                {executionError}
+              </pre>
+            </div>
+          )}
+        </div>
+
+        <div
+          style={{
+            marginTop: "16px",
+            padding: "10px",
+            backgroundColor: "#F5F5F5",
+            borderRadius: "4px",
+            fontSize: "12px",
+            color: "#666",
+          }}>
+          <strong>Highlighted Code:</strong>
+          <pre
+            style={{
+              margin: "8px 0 0 0",
+              padding: "8px",
+              backgroundColor: "white",
+              borderRadius: "3px",
+              fontSize: "12px",
+              overflow: "auto",
+              border: "1px solid #E0E0E0",
+            }}>
+            {highlightedCode || "(No code selected)"}
+          </pre>
+        </div>
+      </div>
+    </div>
+  );
+};
+const OutputVisualizer: React.FC<AnnotationEditorProps> = (props) => {
+  const [predictedOutput, setPredictedOutput] = useState(
+    props.value.metadata.predictedOutput || ""
+  );
+  const [variableChanges, setVariableChanges] = useState(
+    props.value.metadata.variableChanges || []
+  );
+  const [llmExplanation, setLlmExplanation] = useState(props.value.metadata.llmExplanation || "");
+  const [confidence, setConfidence] = useState(props.value.metadata.confidence || "medium");
+  const [isAnalyzing, setIsAnalyzing] = useState(false);
+  const [testInputs, setTestInputs] = useState(props.value.metadata.testInputs || "");
+  const [actualOutput, setActualOutput] = useState(props.value.metadata.actualOutput || null);
+  const [executionError, setExecutionError] = useState(props.value.metadata.executionError || null);
+
+  // Get the highlighted code and document context
+  const highlightedCode = props.utils.getText();
+  const documentText = props.value.document || "";
+
+  // Save state to metadata
+  useEffect(() => {
+    props.utils.setMetadata({
+      predictedOutput,
+      variableChanges,
+      llmExplanation,
+      confidence,
+      testInputs,
+      actualOutput,
+      executionError,
+    });
+  }, [
+    predictedOutput,
+    variableChanges,
+    llmExplanation,
+    confidence,
+    testInputs,
+    actualOutput,
+    executionError,
+  ]);
+
+  // Analyze code and predict output
+  const analyzeCode = async () => {
+    setIsAnalyzing(true);
+
+    // Simulate analysis (in real implementation, this would call an LLM API)
+    setTimeout(() => {
+      const code = highlightedCode.trim();
+
+      // Check if it's the quickSort function
+      if (code.includes("quickSort") && code.includes("partition")) {
+        setPredictedOutput("A sorted version of the input array 'arr'");
+        setVariableChanges([
+          {
+            variable: "arr",
+            before: "The input array passed to quickSort",
+            after: "The sorted version of the input array",
+          },
+        ]);
+        setLlmExplanation(
+          "The highlighted 'quickSort' function sorts the input array 'arr' in-place using the partitioning logic defined in the 'partition' function. The 'arr' variable is modified directly during the sorting process."
+        );
+        setConfidence("high");
+      }
+      // Check if it's the partition function
+      else if (code.includes("partition") && code.includes("pivot")) {
+        setPredictedOutput(
+          "The index position where the pivot element is placed after partitioning"
+        );
+        setVariableChanges([
+          {
+            variable: "arr",
+            before: "The array segment between low and high indices",
+            after: "Rearranged with elements less than pivot on left, greater on right",
+          },
+          {
+            variable: "i",
+            before: "Initialized to low - 1",
+            after: "Final position before the pivot",
+          },
+        ]);
+        setLlmExplanation(
+          "The 'partition' function rearranges the array segment between 'low' and 'high' indices, using the last element as a pivot. It returns the final position of the pivot after partitioning."
+        );
+        setConfidence("high");
+      }
+      // Generic function detection
+      else if (code.includes("function") || code.includes("=>")) {
+        setPredictedOutput("Function output depends on input parameters");
+        setVariableChanges([]);
+        setLlmExplanation(
+          "This appears to be a function definition. The actual output will depend on the input parameters provided when the function is called."
+        );
+        setConfidence("low");
+      }
+      // Default case
+      else {
+        setPredictedOutput("Code execution result");
+        setVariableChanges([]);
+        setLlmExplanation(
+          "The highlighted code performs operations. Specific output depends on the context and any variables it uses."
+        );
+        setConfidence("low");
+      }
+
+      setIsAnalyzing(false);
+    }, 1000);
+  };
+
+  // Execute code with test inputs
+  const executeCode = async () => {
+    if (!testInputs.trim()) {
+      setExecutionError("Please provide test inputs to execute the function");
+      return;
+    }
+
+    try {
+      const code = highlightedCode.trim();
+      let executionCode = code;
+
+      // Detect if it's a function and create test call
+      const functionMatch = code.match(/function\s+(\w+)/);
+      if (functionMatch) {
+        executionCode = `${code}\n\n${functionMatch[1]}(${testInputs})`;
+      }
+
+      const asyncFunction = new Function(`
+            'use strict';
+            return (async () => {
+              ${executionCode}
+            })();
+          `);
+
+      const result = await asyncFunction();
+
+      if (result === undefined) {
+        setActualOutput("undefined (no return value)");
+      } else if (result === null) {
+        setActualOutput("null");
+      } else if (typeof result === "object") {
+        setActualOutput(JSON.stringify(result, null, 2));
+      } else {
+        setActualOutput(String(result));
+      }
+      setExecutionError(null);
+    } catch (err) {
+      setExecutionError(err instanceof Error ? err.message : String(err));
+      setActualOutput(null);
+    }
+  };
+
+  const getConfidenceColor = () => {
+    switch (confidence) {
+      case "high":
+        return "#22c55e";
+      case "medium":
+        return "#f59e0b";
+      case "low":
+        return "#ef4444";
+      default:
+        return "#6b7280";
+    }
+  };
+
+  return (
+    <div
+      style={{
+        fontFamily: "-apple-system, BlinkMacSystemFont, 'Segoe UI', Roboto, sans-serif",
+        fontSize: "14px",
+        lineHeight: "1.6",
+        color: "#1f2937",
+      }}>
+      {/* Predicted Output Section */}
+      <div
+        style={{
+          backgroundColor: "#f9fafb",
+          padding: "16px",
+          borderRadius: "8px",
+          marginBottom: "16px",
+        }}>
+        <div
+          style={{
+            fontWeight: "600",
+            marginBottom: "8px",
+            fontSize: "15px",
+          }}>
+          Predicted return / output:
+        </div>
+        <div
+          style={{
+            backgroundColor: "white",
+            padding: "12px",
+            borderRadius: "6px",
+            border: "1px solid #e5e7eb",
+          }}>
+          {predictedOutput || (
+            <span style={{ color: "#9ca3af", fontStyle: "italic" }}>
+              Click "Analyze Code" to predict output
+            </span>
+          )}
+        </div>
+      </div>
+
+      {/* Variable Changes Section */}
+      <div
+        style={{
+          backgroundColor: "#f9fafb",
+          padding: "16px",
+          borderRadius: "8px",
+          marginBottom: "16px",
+        }}>
+        <div
+          style={{
+            fontWeight: "600",
+            marginBottom: "12px",
+            fontSize: "15px",
+          }}>
+          Predicted variable changes:
+        </div>
+        {variableChanges.length > 0 ? (
+          <table
+            style={{
+              width: "100%",
+              backgroundColor: "white",
+              borderRadius: "6px",
+              overflow: "hidden",
+              border: "1px solid #e5e7eb",
+            }}>
+            <thead>
+              <tr style={{ backgroundColor: "#f3f4f6" }}>
+                <th
+                  style={{
+                    padding: "10px",
+                    textAlign: "left",
+                    fontWeight: "600",
+                    borderBottom: "1px solid #e5e7eb",
+                    width: "20%",
+                  }}>
+                  Variable
+                </th>
+                <th
+                  style={{
+                    padding: "10px",
+                    textAlign: "left",
+                    fontWeight: "600",
+                    borderBottom: "1px solid #e5e7eb",
+                    width: "40%",
+                  }}>
+                  Before
+                </th>
+                <th
+                  style={{
+                    padding: "10px",
+                    textAlign: "left",
+                    fontWeight: "600",
+                    borderBottom: "1px solid #e5e7eb",
+                    width: "40%",
+                  }}>
+                  After
+                </th>
+              </tr>
+            </thead>
+            <tbody>
+              {variableChanges.map((change: any, index: number) => (
+                <tr key={index}>
+                  <td
+                    style={{
+                      padding: "10px",
+                      fontFamily: "monospace",
+                      fontSize: "13px",
+                      fontWeight: "500",
+                    }}>
+                    {change.variable}
+                  </td>
+                  <td
+                    style={{
+                      padding: "10px",
+                      fontSize: "13px",
+                      color: "#4b5563",
+                    }}>
+                    {change.before}
+                  </td>
+                  <td
+                    style={{
+                      padding: "10px",
+                      fontSize: "13px",
+                      color: "#4b5563",
+                    }}>
+                    {change.after}
+                  </td>
+                </tr>
+              ))}
+            </tbody>
+          </table>
+        ) : (
+          <div
+            style={{
+              backgroundColor: "white",
+              padding: "12px",
+              borderRadius: "6px",
+              border: "1px solid #e5e7eb",
+              color: "#9ca3af",
+              fontStyle: "italic",
+            }}>
+            No variable changes predicted
+          </div>
+        )}
+      </div>
+
+      {/* LLM Explanation Section */}
+      <div
+        style={{
+          backgroundColor: "#f9fafb",
+          padding: "16px",
+          borderRadius: "8px",
+          marginBottom: "16px",
+        }}>
+        <div
+          style={{
+            fontWeight: "600",
+            marginBottom: "8px",
+            fontSize: "15px",
+          }}>
+          LLM explanation:
+        </div>
+        <div
+          style={{
+            backgroundColor: "white",
+            padding: "12px",
+            borderRadius: "6px",
+            border: "1px solid #e5e7eb",
+            color: "#374151",
+          }}>
+          {llmExplanation || (
+            <span style={{ color: "#9ca3af", fontStyle: "italic" }}>
+              Click "Analyze Code" to get explanation
+            </span>
+          )}
+        </div>
+        {llmExplanation && (
+          <div
+            style={{
+              marginTop: "8px",
+              fontSize: "13px",
+              display: "flex",
+              alignItems: "center",
+              gap: "6px",
+            }}>
+            <span style={{ color: "#6b7280" }}>Confidence:</span>
+            <span
+              style={{
+                color: getConfidenceColor(),
+                fontWeight: "600",
+              }}>
+              {confidence}
+            </span>
+          </div>
+        )}
+      </div>
+
+      {/* Control Buttons */}
+      <div
+        style={{
+          display: "flex",
+          gap: "12px",
+          marginBottom: "16px",
+        }}>
+        <button
+          onClick={analyzeCode}
+          disabled={isAnalyzing || !highlightedCode.trim()}
+          style={{
+            padding: "8px 20px",
+            backgroundColor: isAnalyzing ? "#e5e7eb" : "#3b82f6",
+            color: isAnalyzing ? "#9ca3af" : "white",
+            border: "none",
+            borderRadius: "6px",
+            cursor: isAnalyzing || !highlightedCode.trim() ? "not-allowed" : "pointer",
+            fontSize: "14px",
+            fontWeight: "500",
+            transition: "background-color 0.2s",
+          }}>
+          {isAnalyzing ? "Analyzing..." : "Analyze Code"}
+        </button>
+      </div>
+
+      {/* Test Execution Section (Optional) */}
+      <details style={{ marginTop: "20px" }}>
+        <summary
+          style={{
+            cursor: "pointer",
+            fontSize: "14px",
+            fontWeight: "600",
+            color: "#4b5563",
+            marginBottom: "12px",
+            userSelect: "none",
+          }}>
+          Test Execution (Optional)
+        </summary>
+
+        <div
+          style={{
+            backgroundColor: "#f9fafb",
+            padding: "16px",
+            borderRadius: "8px",
+            marginTop: "8px",
+          }}>
+          <div style={{ marginBottom: "12px" }}>
+            <label
+              style={{
+                display: "block",
+                marginBottom: "6px",
+                fontSize: "13px",
+                fontWeight: "500",
+                color: "#374151",
+              }}>
+              Test Inputs:
+            </label>
+            <input
+              value={testInputs}
+              onChange={(e) => setTestInputs(e.target.value)}
+              placeholder="e.g., [3, 5, 2, 8, 1], 0, 4"
+              style={{
+                width: "100%",
+                padding: "8px",
+                borderRadius: "4px",
+                border: "1px solid #d1d5db",
+                fontSize: "13px",
+                fontFamily: "monospace",
+              }}
+            />
+          </div>
+
+          <button
+            onClick={executeCode}
+            style={{
+              padding: "6px 16px",
+              backgroundColor: "#10b981",
+              color: "white",
+              border: "none",
+              borderRadius: "4px",
+              cursor: "pointer",
+              fontSize: "13px",
+              fontWeight: "500",
+              marginBottom: "12px",
+            }}>
+            Execute with Test Inputs
+          </button>
+
+          {actualOutput !== null && (
+            <div
+              style={{
+                backgroundColor: "white",
+                padding: "10px",
+                borderRadius: "4px",
+                border: "1px solid #d1d5db",
+                marginTop: "8px",
+              }}>
+              <div
+                style={{
+                  fontSize: "12px",
+                  fontWeight: "600",
+                  marginBottom: "4px",
+                  color: "#059669",
+                }}>
+                Actual Output:
+              </div>
+              <pre
+                style={{
+                  margin: 0,
+                  fontFamily: "monospace",
+                  fontSize: "12px",
+                  whiteSpace: "pre-wrap",
+                  color: "#1f2937",
+                }}>
+                {actualOutput}
+              </pre>
+            </div>
+          )}
+
+          {executionError && (
+            <div
+              style={{
+                backgroundColor: "#fef2f2",
+                padding: "10px",
+                borderRadius: "4px",
+                border: "1px solid #fecaca",
+                marginTop: "8px",
+              }}>
+              <div
+                style={{
+                  fontSize: "12px",
+                  fontWeight: "600",
+                  marginBottom: "4px",
+                  color: "#dc2626",
+                }}>
+                Execution Error:
+              </div>
+              <pre
+                style={{
+                  margin: 0,
+                  fontFamily: "monospace",
+                  fontSize: "11px",
+                  whiteSpace: "pre-wrap",
+                  color: "#991b1b",
+                }}>
+                {executionError}
+              </pre>
+            </div>
+          )}
+        </div>
+      </details>
+
+      {/* Code Reference */}
+      <details style={{ marginTop: "16px" }}>
+        <summary
+          style={{
+            cursor: "pointer",
+            fontSize: "13px",
+            color: "#6b7280",
+            userSelect: "none",
+          }}>
+          View highlighted code
+        </summary>
+        <pre
+          style={{
+            marginTop: "8px",
+            padding: "10px",
+            backgroundColor: "#f3f4f6",
+            borderRadius: "4px",
+            fontSize: "11px",
+            overflow: "auto",
+            fontFamily: "monospace",
+            color: "#374151",
+          }}>
+          {highlightedCode || "(No code selected)"}
+        </pre>
+      </details>
+    </div>
+  );
+};
+const FormalSpecification: React.FC<AnnotationEditorProps> = (props) => {
+  const [highlightedSpec, setHighlightedSpec] = useState({ formal: "", simple: "" });
+  const [isGenerating, setIsGenerating] = useState(false);
+  const [error, setError] = useState<string | null>(null);
+  const [expanded, setExpanded] = useState({ highlighted: true });
+
+  const highlightedCode = props.utils.getText() || "";
+
+  // persist specs to metadata
+  useEffect(() => {
+    props.utils.setMetadata({ highlightedSpec });
+  }, [highlightedSpec]);
+
+  const basePrompt = `
+  You are a formal methods assistant that writes CORRECT formal program specifications
+  for JavaScript code using clear mathematical notation.
+
+  Given the input code, produce two synchronized outputs:
+
+  1. "formal" — a formal specification suitable for program verification,
+    including preconditions, postconditions, invariants, and input-output relations,
+    using symbols like ∀, ∃, ⇒, ∧, ∨, =, and set-builder notation when needed.
+
+  2. "simple" — a plain-English presentation of the same specification (non-mathematical).
+
+  Respond with ONLY valid JSON of this form:
+  {
+    "formal": "...",
+    "simple": "..."
+  }
+  `;
+
+  // normalize LLM output
+  const extractTextFromResponse = (resp: any): string => {
+    if (typeof resp === "string") return resp;
+    if (resp && typeof resp === "object") {
+      if (resp.content) return resp.content;
+      if (resp.text) return resp.text;
+      if (Array.isArray(resp.choices) && resp.choices[0]?.message?.content)
+        return resp.choices[0].message.content;
+      if (Array.isArray(resp)) return resp.map((r) => r.content || r.text || "").join("\n");
+      try {
+        return JSON.stringify(resp);
+      } catch {
+        return String(resp);
+      }
+    }
+    return String(resp);
+  };
+
+  // parse JSON safely
+  const tryParseSpecFromText = (text: string) => {
+    const trimmed = text.trim();
+    try {
+      return { parsed: JSON.parse(trimmed) };
+    } catch {
+      const match = trimmed.match(/\{[\s\S]*\}/);
+      if (match) {
+        try {
+          return { parsed: JSON.parse(match[0]) };
+        } catch {
+          return { error: "Found JSON-like text but parsing failed." };
+        }
+      }
+      return { error: "No valid JSON found in response." };
+    }
+  };
+
+  const generateSpec = async () => {
+    const code = highlightedCode.trim();
+    if (!code) {
+      setError("No code selected for specification generation.");
+      return;
+    }
+
+    setIsGenerating(true);
+    setError(null);
+
+    const prompt: ChatMessage[] = [
+      { role: "system", content: basePrompt },
+      {
+        role: "user",
+        content: `Here is the highlighted code section:\n\n${code}\n\nPlease output JSON with keys "formal" and "simple".`,
+      },
+    ];
+
+    try {
+      const resp = await lmApi.chat(prompt, {
+        vendor: "copilot",
+        family: "gpt-4o",
+        temperature: 0.2,
+      });
+      const text = extractTextFromResponse(resp);
+      const { parsed, error: parseErr } = tryParseSpecFromText(text);
+
+      if (parseErr || !parsed?.formal || !parsed?.simple) {
+        setError("Unable to parse LLM response. Please retry.");
+        return;
+      }
+
+      const cleanSpec = {
+        formal: parsed.formal.trim(),
+        simple: parsed.simple.trim(),
+      };
+
+      setHighlightedSpec(cleanSpec);
+    } catch (err: any) {
+      setError(`Error generating specification: ${err.message || String(err)}`);
+    } finally {
+      setIsGenerating(false);
+    }
+  };
+
+  const renderSplitBox = (title: string, spec: { formal: string; simple: string }) => {
+    const isOpen = expanded.highlighted;
+    return (
+      <details
+        open={isOpen}
+        onToggle={(e) =>
+          setExpanded((prev) => ({
+            ...prev,
+            highlighted: (e.target as HTMLDetailsElement).open,
+          }))
+        }
+        style={{
+          marginBottom: "16px",
+          border: "1px solid #ccc",
+          borderRadius: "6px",
+          backgroundColor: "#fafafa",
+          overflow: "hidden",
+        }}>
+        <summary
+          style={{
+            cursor: "pointer",
+            fontWeight: 600,
+            fontSize: "15px",
+            padding: "10px 12px",
+            backgroundColor: "#f3f4f6",
+            borderBottom: "1px solid #ddd",
+            userSelect: "none",
+          }}>
+          {title}
+        </summary>
+        <div style={{ display: "flex", minHeight: "180px" }}>
+          <div
+            style={{
+              flex: 1,
+              padding: "12px",
+              backgroundColor: "#f9fafb",
+              borderRight: "1px solid #ddd",
+              fontFamily: "monospace",
+              fontSize: "13px",
+              whiteSpace: "pre-wrap",
+            }}>
+            <strong>Formal Specification</strong>
+            <hr />
+            {spec.formal || <span style={{ color: "#999" }}>No specification yet</span>}
+          </div>
+          <div
+            style={{
+              flex: 1,
+              padding: "12px",
+              backgroundColor: "#ffffff",
+              fontFamily: "Poppins, sans-serif",
+              fontSize: "13px",
+              lineHeight: "1.5",
+              whiteSpace: "pre-wrap",
+            }}>
+            <strong>Plain-English Explanation</strong>
+            <hr />
+            {spec.simple || <span style={{ color: "#999" }}>No explanation yet</span>}
+          </div>
+        </div>
+      </details>
+    );
+  };
+
+  return (
+    <div
+      style={{
+        fontFamily: "Poppins, sans-serif",
+        fontSize: "14px",
+        color: "#333",
+        padding: "12px",
+      }}>
+      <h3 style={{ marginBottom: "12px", fontWeight: "600" }}>
+        🧮 Formal Program Specification Generator
+      </h3>
+
+      <div
+        style={{
+          display: "flex",
+          gap: "10px",
+          marginBottom: "16px",
+          flexWrap: "wrap",
+        }}>
+        <button
+          onClick={() => generateSpec()}
+          disabled={isGenerating}
+          style={{
+            padding: "8px 16px",
+            backgroundColor: "#2563eb",
+            color: "white",
+            border: "none",
+            borderRadius: "4px",
+            cursor: isGenerating ? "not-allowed" : "pointer",
+            fontWeight: "500",
+          }}>
+          {isGenerating ? "Generating..." : "Generate Specification"}
+        </button>
+      </div>
+
+      {error && (
+        <div
+          style={{
+            backgroundColor: "#fef2f2",
+            border: "1px solid #fecaca",
+            color: "#b91c1c",
+            padding: "10px",
+            borderRadius: "4px",
+            marginBottom: "16px",
+            fontSize: "13px",
+          }}>
+          ⚠️ {error}
+        </div>
+      )}
+
+      {renderSplitBox("Specification for Highlighted Code", highlightedSpec)}
+    </div>
+  );
+};
+const Generator: React.FC<AnnotationEditorProps> = (props) => {
+  // State management
+  const [userInput, setUserInput] = useState(props.value.metadata.userInput || "");
+  const [generatedCode, setGeneratedCode] = useState(props.value.metadata.generatedCode || "");
+  const [isGenerating, setIsGenerating] = useState(false);
+  const [error, setError] = useState<string | null>(null);
+  const [useMock, setUseMock] = useState(false);
+  const [apiDiagnostics, setApiDiagnostics] = useState<string>("");
+  const [GeneratedComponent, setGeneratedComponent] =
+    useState<React.FC<AnnotationEditorProps> | null>(null);
+
+  const isMounted = useRef(true);
+
+  // Fallback mock API - only used when real API completely fails
+  // This does NOT generate predetermined templates - it shows the actual error
+  const fallbackMockLmApi = {
+    chat: async (messages: any, options?: any, errorDetails?: string) => {
+      console.log("[FallbackMockAPI] Real API failed - showing error component with details");
+
+      // Escape the error message for safe inclusion in JavaScript string
+      const safeErrorDetails = (errorDetails || "Unknown error")
+        .replace(/\\/g, "\\\\")
+        .replace(/'/g, "\\'")
+        .replace(/"/g, '\\"')
+        .replace(/\n/g, "\\n")
+        .replace(/\r/g, "\\r");
+
+      // Return an error component that displays the actual error
+      return `
+const [showDetails, setShowDetails] = useState(false);
+
+console.log('[FallbackComponent] Real API failed, showing error');
+
+return React.createElement('div',
+  { style: { padding: '10px', fontFamily: 'Poppins, sans-serif' } },
+  React.createElement('div',
+    { style: { padding: '12px', backgroundColor: '#FED9CC', border: '2px solid #D83B01', borderRadius: '6px', marginBottom: '10px' } },
+    React.createElement('h3', 
+      { style: { ...commonTextStyle, marginBottom: '10px', color: '#D83B01', fontSize: '16px' } },
+      '⚠️ API Error'
+    ),
+    React.createElement('p',
+      { style: { ...commonTextStyle, fontSize: '13px', marginBottom: '10px' } },
+      'The component generation API failed. See error details below:'
+    ),
+    React.createElement('div',
+      { style: { marginTop: '10px', marginBottom: '10px' } },
+      React.createElement('button',
+        {
+          onClick: () => setShowDetails(!showDetails),
+          style: {
+            padding: '6px 12px',
+            backgroundColor: '#D83B01',
+            color: 'white',
+            border: 'none',
+            borderRadius: '4px',
+            cursor: 'pointer',
+            fontSize: '12px'
+          }
+        },
+        showDetails ? '▼ Hide Error Details' : '▶ Show Error Details'
+      )
+    ),
+    showDetails && React.createElement('pre',
+      {
+        style: {
+          marginTop: '10px',
+          padding: '10px',
+          backgroundColor: '#fff',
+          border: '1px solid #D83B01',
+          borderRadius: '4px',
+          fontSize: '11px',
+          overflow: 'auto',
+          maxHeight: '200px',
+          fontFamily: 'monospace',
+          whiteSpace: 'pre-wrap',
+          wordBreak: 'break-word'
+        }
+      },
+      '${safeErrorDetails}'
+    )
+  ),
+  React.createElement('div',
+    { style: { padding: '10px', backgroundColor: '#F0F0F0', borderRadius: '4px', fontSize: '12px' } },
+    React.createElement('p',
+      { style: { ...commonTextStyle, fontWeight: 'bold', marginBottom: '8px' } },
+      'Your request:'
+    ),
+    React.createElement('p',
+      { style: { ...commonTextStyle, fontSize: '12px', fontStyle: 'italic', marginBottom: '10px' } },
+      props.value.metadata.userInput || 'No request provided'
+    ),
+    React.createElement('p',
+      { style: { ...commonTextStyle, fontWeight: 'bold', marginBottom: '8px' } },
+      'Highlighted text:'
+    ),
+    React.createElement('pre',
+      { style: { ...commonTextStyle, fontSize: '11px', backgroundColor: '#fff', padding: '8px', borderRadius: '4px', overflow: 'auto', maxHeight: '100px' } },
+      props.utils.getText() || 'No text highlighted'
+    )
+  )
+);
+      `.trim();
+    },
+  };
+
+  useEffect(() => {
+    // Comprehensive API diagnostics
+    const diagnostics = [];
+
+    diagnostics.push("=== API Diagnostics ===");
+    diagnostics.push(`vscode: ${typeof vscode} ${vscode ? "✓" : "✗"}`);
+    diagnostics.push(`lmApi: ${typeof lmApi} ${lmApi ? "✓" : "✗"}`);
+
+    if (lmApi) {
+      diagnostics.push(
+        `lmApi.chat: ${typeof lmApi.chat} ${typeof lmApi.chat === "function" ? "✓" : "✗"}`
+      );
+    }
+
+    diagnostics.push(
+      `fallbackMockLmApi: ${typeof fallbackMockLmApi} ${fallbackMockLmApi ? "✓" : "✗"}`
+    );
+
+    const diagText = diagnostics.join("\n");
+    setApiDiagnostics(diagText);
+    console.log(diagText);
+
+    // Only use mock if the real API is not available
+    const lmApiAvailable =
+      typeof lmApi !== "undefined" && lmApi !== null && typeof lmApi.chat === "function";
+
+    if (!lmApiAvailable) {
+      console.warn("[Generator] Real lmApi not available - fallback mode enabled");
+      setUseMock(true);
+    } else {
+      console.log("[Generator] Real lmApi is available");
+      setUseMock(false);
+    }
+
+    return () => {
+      isMounted.current = false;
+    };
+  }, []);
+
+  // Load existing generated component on mount
+  useEffect(() => {
+    if (generatedCode && isMounted.current) {
+      try {
+        compileComponent(generatedCode);
+      } catch (err) {
+        console.error("[Generator] Failed to compile existing code:", err);
+      }
+    }
+  }, []);
+
+  // Save state to metadata
+  useEffect(() => {
+    props.utils.setMetadata({
+      userInput,
+      generatedCode,
+    });
+  }, [userInput, generatedCode]);
+
+  // Get document context
+  const anchorText = props.utils.getText();
+  const documentText = props.value.document || "";
+  const startPos = props.value.start;
+  const endPos = props.value.end;
+
+  const createFormattedDocument = () => {
+    if (!documentText) return "";
+
+    const before = documentText.substring(0, startPos);
+    const highlighted = documentText.substring(startPos, endPos);
+    const after = documentText.substring(endPos);
+
+    return `${before}<<<HIGHLIGHTED>${highlighted}</HIGHLIGHTED>>>${after}`;
+  };
+
+  const generateAnnotation = async () => {
+    if (!userInput.trim()) {
+      setError("Please describe what you want the annotation to do");
+      return;
+    }
+
+    setIsGenerating(true);
+    setError(null);
+
+    try {
+      const formattedDocument = createFormattedDocument();
+
+      const prompt: ChatMessage[] = [
+        {
+          role: "system",
+          content: `You are an expert React developer creating annotation components for a code annotation system. 
+
+CONTEXT:
+- You will receive a description of what the annotation should do
+- You have access to the highlighted code/text and surrounding document context
+- The annotation component receives props of type AnnotationEditorProps with these key utilities:
+  * props.utils.getText() - gets the highlighted text
+  * props.utils.setText(newText) - updates the highlighted text
+  * props.utils.setMetadata(obj) - persists data across sessions
+  * props.value.metadata - retrieves persisted data
+  * props.value.document - the full document text for context
+  * props.value.start/end - position of highlighted text
+
+CRITICAL REQUIREMENT - NO JSX:
+You MUST use React.createElement() instead of JSX syntax because the code will be compiled without a JSX transformer.
+DO NOT use angle brackets like <div>, <button>, etc.
+Instead use: React.createElement('div', { style: {...} }, 'content')
+
+REQUIREMENTS:
+1. Generate ONLY the component function body using React.createElement
+2. Do NOT include: imports, export statements, or the component function declaration
+3. Use React hooks (useState, useEffect, useRef) as needed - they're available from React destructuring
+4. Store all state in metadata using props.utils.setMetadata() for persistence
+5. Use the commonTextStyle constant for consistent styling: { fontFamily: "Poppins, sans-serif", fontSize: "14px", color: "black" }
+6. Include comprehensive console.log statements for debugging with format: console.log('[ComponentName] message', data)
+7. Handle errors gracefully with try-catch blocks
+8. The lmApi is available with this EXACT signature:
+   const response = await lmApi.chat(messages, { vendor: 'copilot', family: 'gpt-4o', temperature: 0.32 });
+   IMPORTANT: lmApi.chat() returns a STRING directly, NOT an object. Use it like: const text = await lmApi.chat(messages, options);
+9. Use props.value.document to understand code context for better defaults and behavior
+10. Keep explanations and messages concise and user-friendly
+11. GENERATE EXACTLY WHAT THE USER REQUESTS - do not fall back to predetermined templates
+
+OUTPUT FORMAT:
+Return ONLY valid JavaScript code using React.createElement().
+Start directly with useState/useEffect declarations or the return statement.
+DO NOT wrap code in markdown code blocks.
+
+EXAMPLE OUTPUT STRUCTURE:
+const [value, setValue] = useState(props.value.metadata.value || '');
+console.log('[ComponentName] Initialized with value:', value);
+
+useEffect(() => {
+  props.utils.setMetadata({ value });
+}, [value]);
+
+const handleAction = async () => {
+  console.log('[ComponentName] Action triggered');
+  try {
+    const result = await lmApi.chat([
+      { role: 'system', content: 'You are helpful.' },
+      { role: 'user', content: 'Hello' }
+    ], { vendor: 'copilot', family: 'gpt-4o', temperature: 0.5 });
+    console.log('[ComponentName] Got result:', result);
+  } catch (error) {
+    console.error('[ComponentName] Error:', error);
+  }
+};
+
+return React.createElement('div', 
+  { style: { padding: "10px", fontFamily: "Poppins, sans-serif" } },
+  React.createElement('button', 
+    { onClick: handleAction, style: commonTextStyle },
+    'Click Me'
+  ),
+  React.createElement('p', { style: commonTextStyle }, value)
+);`,
+        },
+        {
+          role: "user",
+          content: `Create an annotation component based on this EXACT description:
+${userInput}
+
+Document context (highlighted section marked):
+${formattedDocument || "No document context available"}
+
+Highlighted text:
+${anchorText || "No text highlighted"}
+
+IMPORTANT: Generate a component that fulfills the EXACT request above. Do not use predetermined templates or generic components. Create custom functionality that matches what the user specifically asked for.
+
+Generate the component implementation now.`,
+        },
+      ];
+
+      console.log("[Generator] Starting generation...");
+      console.log("[Generator] Force fallback mode:", useMock);
+      console.log("[Generator] User request:", userInput);
+
+      let response: string;
+      let apiUsed = "unknown";
+
+      if (useMock) {
+        console.log("[Generator] Using fallback API (manual override - NOT RECOMMENDED)");
+        response = await fallbackMockLmApi.chat(
+          prompt,
+          undefined,
+          "Manual fallback mode enabled - real API was not attempted"
+        );
+        apiUsed = "fallback-manual";
+      } else {
+        console.log("[Generator] Attempting real lmApi...");
+        console.log("[Generator] lmApi type:", typeof lmApi);
+        console.log("[Generator] lmApi.chat type:", typeof lmApi?.chat);
+
+        try {
+          const startTime = Date.now();
+          response = await lmApi.chat(prompt, {
+            vendor: "copilot",
+            family: "gpt-4o",
+            temperature: 0.3,
+          });
+          const elapsed = Date.now() - startTime;
+          console.log(`[Generator] Real API succeeded in ${elapsed}ms`);
+          apiUsed = "real";
+        } catch (apiError: unknown) {
+          console.error("[Generator] Real API failed:", apiError);
+          console.error("[Generator] Error type:", (apiError as any)?.constructor?.name);
+          console.error(
+            "[Generator] Error message:",
+            apiError instanceof Error ? apiError.message : String(apiError)
+          );
+          console.log("[Generator] Falling back to error component");
+
+          // Format the error details for display
+          let errorDetails = "";
+          if (apiError instanceof Error) {
+            errorDetails = `Error: ${apiError.message}\n\nStack trace:\n${
+              apiError.stack || "No stack trace available"
+            }`;
+          } else {
+            errorDetails = `Error: ${String(apiError)}\n\nType: ${
+              (apiError as any)?.constructor?.name || "unknown"
+            }`;
+          }
+
+          // Add any additional error properties
+          if (typeof apiError === "object" && apiError !== null) {
+            const errorObj = apiError as any;
+            const extraProps = Object.keys(errorObj).filter(
+              (k) => k !== "message" && k !== "stack" && k !== "name"
+            );
+            if (extraProps.length > 0) {
+              errorDetails += "\n\nAdditional details:\n";
+              extraProps.forEach((prop) => {
+                errorDetails += `${prop}: ${JSON.stringify(errorObj[prop], null, 2)}\n`;
+              });
+            }
+          }
+
+          response = await fallbackMockLmApi.chat(prompt, undefined, errorDetails);
+          apiUsed = "fallback-auto";
+        }
+      }
+
+      console.log("[Generator] API used:", apiUsed);
+      console.log("[Generator] Response length:", response?.length);
+      console.log("[Generator] Response preview:", response?.substring(0, 100));
+
+      // Extract code from response (remove markdown code blocks if present)
+      let code = response.trim();
+      const codeBlockMatch = code.match(/```(?:javascript|typescript|jsx|tsx)?\n([\s\S]*?)\n```/);
+      if (codeBlockMatch) {
+        code = codeBlockMatch[1].trim();
+        console.log("[Generator] Extracted code from markdown block");
+      }
+
+      console.log("[Generator] Final code length:", code.length);
+
+      if (isMounted.current) {
+        setGeneratedCode(code);
+        compileComponent(code);
+        console.log("[Generator] Component compiled successfully");
+      }
+    } catch (err) {
+      const errorMsg =
+        err instanceof Error ? err.message : "An error occurred while generating the annotation";
+      console.error("[Generator] Error:", errorMsg, err);
+      if (isMounted.current) {
+        setError(errorMsg);
+      }
+    } finally {
+      if (isMounted.current) {
+        setIsGenerating(false);
+      }
+    }
+  };
+
+  const compileComponent = (code: string) => {
+    try {
+      console.log("[Generator] Compiling component...");
+
+      const commonTextStyle = {
+        fontFamily: "Poppins, sans-serif",
+        fontSize: "14px",
+        color: "black",
+      };
+
+      // Create a function that returns a React component
+      const componentFunction = new Function(
+        "React",
+        "props",
+        "lmApi",
+        "mockLmApi",
+        "vscode",
+        "commonTextStyle",
+        `
+        const { useState, useEffect, useRef } = React;
+        ${code}
+        `
+      );
+
+      // Create a wrapper component
+      const WrappedComponent: React.FC<AnnotationEditorProps> = (componentProps) => {
+        return componentFunction(React, componentProps, lmApi, mockLmApi, vscode, commonTextStyle);
+      };
+
+      setGeneratedComponent(() => WrappedComponent);
+      console.log("[Generator] Component compiled and set successfully");
+    } catch (err) {
+      console.error("[Generator] Compilation error:", err);
+      throw new Error(
+        `Failed to compile generated component: ${err instanceof Error ? err.message : String(err)}`
+      );
+    }
+  };
+
+  const resetGenerator = () => {
+    console.log("[Generator] Resetting generator");
+    setGeneratedCode("");
+    setGeneratedComponent(null);
+    setError(null);
+  };
+
+  // If we have a generated component, render it
+  if (GeneratedComponent) {
+    return (
+      <div style={{ padding: "10px", fontFamily: "Poppins, sans-serif" }}>
+        <div
+          style={{
+            marginBottom: "10px",
+            padding: "8px",
+            backgroundColor: "#E8F5E9",
+            border: "1px solid #4CAF50",
+            borderRadius: "4px",
+            fontSize: "12px",
+            display: "flex",
+            justifyContent: "space-between",
+            alignItems: "center",
+          }}>
+          <span>✓ Generated annotation active</span>
+          <button
+            onClick={resetGenerator}
+            style={{
+              padding: "4px 8px",
+              backgroundColor: "#f44336",
+              color: "white",
+              border: "none",
+              borderRadius: "4px",
+              cursor: "pointer",
+              fontSize: "12px",
+            }}>
+            Reset
+          </button>
+        </div>
+        <GeneratedComponent {...props} />
+      </div>
+    );
+  }
+
+  // Otherwise, show the input interface
+  return (
+    <div style={{ padding: "10px", fontFamily: "Poppins, sans-serif" }}>
+      {apiDiagnostics && (
+        <details style={{ marginBottom: "15px", fontSize: "11px", color: "#666" }}>
+          <summary style={{ cursor: "pointer", fontWeight: "bold" }}>
+            API Diagnostics (click to expand)
+          </summary>
+          <pre
+            style={{
+              marginTop: "8px",
+              padding: "8px",
+              backgroundColor: "#f5f5f5",
+              borderRadius: "4px",
+              overflow: "auto",
+            }}>
+            {apiDiagnostics}
+          </pre>
+        </details>
+      )}
+
+      <div style={{ marginBottom: "12px" }}>
+        <label
+          style={{
+            display: "block",
+            marginBottom: "6px",
+            fontWeight: "bold",
+            fontSize: "14px",
+          }}>
+          Describe the annotation you want to create:
+        </label>
+        <textarea
+          value={userInput}
+          onChange={(e) => setUserInput(e.target.value)}
+          placeholder="Example: Create a color picker that lets me change the hex color value in this code... or Create a timer that counts down from the number in this variable..."
+          style={{
+            width: "100%",
+            padding: "8px",
+            borderRadius: "4px",
+            border: "1px solid #ccc",
+            fontSize: "14px",
+            minHeight: "80px",
+            resize: "vertical",
+            fontFamily: "Poppins, sans-serif",
+          }}
+        />
+      </div>
+
+      <div style={{ marginBottom: "15px", display: "flex", gap: "10px", alignItems: "center" }}>
+        <button
+          onClick={generateAnnotation}
+          disabled={isGenerating || !userInput.trim()}
+          style={{
+            padding: "6px 12px",
+            backgroundColor: isGenerating ? "#cccccc" : "#0078D4",
+            color: "white",
+            border: "none",
+            borderRadius: "4px",
+            cursor: isGenerating ? "default" : "pointer",
+            fontSize: "14px",
+          }}>
+          {isGenerating ? "Generating..." : "Generate"}
+        </button>
+
+        <label
+          style={{
+            display: "flex",
+            alignItems: "center",
+            fontSize: "12px",
+            cursor: "pointer",
+            marginLeft: "10px",
+          }}>
+          <input
+            type="checkbox"
+            checked={useMock}
+            onChange={() => setUseMock(!useMock)}
+            style={{ marginRight: "5px" }}
+          />
+          Force fallback mode (shows error - for testing only)
+        </label>
+
+        <span style={{ fontSize: "11px", color: "#666", marginLeft: "10px" }}>
+          {useMock ? "⚠️ Fallback Mode" : "✓ Real API"}
+        </span>
+      </div>
+
+      {error && (
+        <div
+          style={{
+            color: "#D83B01",
+            backgroundColor: "#FED9CC",
+            padding: "8px",
+            borderRadius: "4px",
+            marginBottom: "12px",
+            fontSize: "14px",
+          }}>
+          {error}
+        </div>
+      )}
+
+      {generatedCode && !GeneratedComponent && (
+        <div
+          style={{
+            marginTop: "15px",
+            padding: "10px",
+            backgroundColor: "#FFF3CD",
+            border: "1px solid #FFC107",
+            borderRadius: "4px",
+            fontSize: "12px",
+          }}>
+          <strong>Generated code (failed to compile):</strong>
+          <pre
+            style={{
+              marginTop: "8px",
+              padding: "8px",
+              backgroundColor: "#F5F5F5",
+              borderRadius: "4px",
+              overflow: "auto",
+              maxHeight: "200px",
+              fontSize: "11px",
+            }}>
+            {generatedCode}
+          </pre>
+        </div>
+      )}
+
+      <div
+        style={{
+          marginTop: "15px",
+          padding: "10px",
+          backgroundColor: "#F0F0F0",
+          borderRadius: "4px",
+          fontSize: "12px",
+          color: "#666",
+        }}>
+        <strong>Tips:</strong>
+        <ul style={{ marginTop: "5px", marginBottom: "0", paddingLeft: "20px" }}>
+          <li>Be specific about what the annotation should do</li>
+          <li>Describe the exact behavior and UI you want</li>
+          <li>Mention if it should interact with the highlighted text</li>
+          <li>State if data should persist across sessions</li>
+          <li>Examples: "rating stars", "color picker", "countdown timer", "progress tracker"</li>
+        </ul>
+      </div>
+    </div>
+  );
+};
+
+export { Generator, FormalSpecification, ExplainInEnglish, OutputVisualizer };
diff --git a/vscode-extension/webview-ui/src/tools.tsx b/vscode-extension/webview-ui/src/tools.tsx
index 8c21ebd..d1e8698 100644
--- a/vscode-extension/webview-ui/src/tools.tsx
+++ b/vscode-extension/webview-ui/src/tools.tsx
@@ -1,121 +1,139 @@
-    import { AnnotationEditorProps } from "./App";
-    import React, { useEffect, useState, useRef  } from "react";
-    import { ObjectInspector } from "react-inspector";
-    import e from "cors";
-    import './tools.css';
-    import LMUnitTest from "./LMUnitTest";
-    import ShowDebuggedExample from "./ShowDebuggedExample";
-    import { ChatMessage, lmApi, mockLmApi } from "./lm-api-client";
-    import { vscode } from "./utilities/vscode";
-
-    type AnnotationType = React.FC<AnnotationEditorProps>
-    interface ImageData {
-      file: File;
-      src: string;
-    }
+import { AnnotationEditorProps } from "./App";
+import React, { useEffect, useState, useRef } from "react";
+import e from "cors";
+import "./tools.css";
+import LMUnitTest from "./LMUnitTest";
+import ShowDebuggedExample from "./ShowDebuggedExample";
+import { ChatMessage, lmApi, mockLmApi } from "./lm-api-client";
+import { vscode } from "./utilities/vscode";
+
+import {
+  Generator,
+  FormalSpecification,
+  ExplainInEnglish,
+  OutputVisualizer,
+} from "./additionalTools";
+
+type AnnotationType = React.FC<AnnotationEditorProps>;
+interface ImageData {
+  file: File;
+  src: string;
+}
+
+const commonTextStyle: React.CSSProperties = {
+  fontFamily: "Poppins, sans-serif",
+  fontSize: "14px",
+  color: "black",
+};
 
-    const commonTextStyle: React.CSSProperties = {
-      fontFamily: "Poppins, sans-serif",
-      fontSize: "14px",
-      color: "black",
-    };
+const ColorPicker: AnnotationType = (props) => {
+  return (
+    <div className="color-picker">
+      <input
+        value={props.value.metadata.colorName}
+        onChange={(e) => props.utils.setMetadata({ colorName: e.target.value })}
+      />
+      <input
+        type="color"
+        value={props.utils.getText()}
+        onChange={(e) => props.utils.setText(e.target.value)}
+      />
+    </div>
+  );
+};
 
-    const ColorPicker: AnnotationType = (props) => {
-      return (
-        <div className="color-picker">
-          <input
-            value={props.value.metadata.colorName}
-            onChange={(e) => props.utils.setMetadata({ colorName: e.target.value })}
-          />
-          <input
-            type="color"
-            value={props.utils.getText()}
-            onChange={(e) => props.utils.setText(e.target.value)}
-          />
-        </div>
-      );
-    };
+const Comment: React.FC<AnnotationEditorProps> = (props) => {
+  type Reply = {
+    datetime: string;
+    text: string;
+  };
 
-    const Comment: React.FC<AnnotationEditorProps> = (props) => {
-      type Reply = {
-        datetime: string;
-        text: string;
-      };
+  const [comment, setComment] = useState(props.value.metadata.comment || "");
+  const [replies, setReplies] = useState<Reply[]>(props.value.metadata.replies || []);
+  const [newReplyText, setNewReplyText] = useState("");
 
-      const [comment, setComment] = useState(props.value.metadata.comment || "");
-      const [replies, setReplies] = useState<Reply[]>(props.value.metadata.replies || []);
-      const [newReplyText, setNewReplyText] = useState("");
+  // useEffect(() => {
+  //   const handler = setTimeout(() => {
+  //     props.utils.setMetadata({ comment, replies });
+  //   }, 300);
 
-      // useEffect(() => {
-      //   const handler = setTimeout(() => {
-      //     props.utils.setMetadata({ comment, replies });
-      //   }, 300);
+  //   return () => {
+  //     clearTimeout(handler);
+  //   };
+  // }, [comment, replies]);
 
-      //   return () => {
-      //     clearTimeout(handler);
-      //   };
-      // }, [comment, replies]);
+  const handleAddReply = () => {
+    if (newReplyText.trim() !== "") {
+      setReplies([...replies, { text: newReplyText, datetime: new Date().toLocaleString() }]);
+      setNewReplyText("");
+    }
+  };
 
-      const handleAddReply = () => {
-        if (newReplyText.trim() !== "") {
-          setReplies([...replies, { text: newReplyText, datetime: new Date().toLocaleString() }]);
-          setNewReplyText("");
-        }
-      };
+  const handleDeleteReply = (index: number) => {
+    const newReplies = replies.filter((_, i) => i !== index);
+    setReplies(newReplies);
+  };
+  // setComment(e.target.value)}
+  return (
+    <div style={{ marginBottom: "10px" }}>
+      <div
+        style={{
+          fontFamily: "Poppins, sans-serif",
+          display: "flex",
+          gap: "10px",
+          alignItems: "center",
+        }}>
+        <div style={{ fontWeight: "bold", fontSize: "12px" }}>Alex Smith</div>
+        <div
+          style={{
+            fontSize: "10px",
+            // align bottom of line
+          }}>
+          Today at 12:00 PM
+        </div>
+      </div>
+      <div style={{ display: "flex" }}>
+        {/* user icon */}
+        <svg
+          xmlns="http://www.w3.org/2000/svg"
+          width="30"
+          height="30"
+          fill="currentColor"
+          viewBox="0 0 64 64"
+          style={{ margin: "10px", marginLeft: "5px" }}>
+          <circle cx="32" cy="32" r="30" fill="none" stroke="#999" stroke-width="2" />
+          <circle cx="32" cy="20" r="12" fill="#ccc" stroke="#999" stroke-width="2" />
+          <path
+            d="M16 52c0-8.8 7.2-16 16-16s16 7.2 16 16v4H16v-4z"
+            fill="#ccc"
+            stroke="#999"
+            stroke-width="2"
+          />
+        </svg>
 
-      const handleDeleteReply = (index: number) => {
-        const newReplies = replies.filter((_, i) => i !== index);
-        setReplies(newReplies);
-      };
-              // setComment(e.target.value)}
-      return (
-        <div style={{ marginBottom: "10px" }}>
-          <div style={{ fontFamily: "Poppins, sans-serif", display: 'flex', gap: '10px', alignItems: 'center' }}>
-            <div style={{ fontWeight: 'bold', fontSize: "12px" }}>Alex Smith</div>
-            <div style={{
-              fontSize: "10px", 
-              // align bottom of line
-            }}>Today at 12:00 PM</div>
-          </div>
-          <div style={{ display: 'flex' }}>
-            {/* user icon */}
-            <svg
-              xmlns="http://www.w3.org/2000/svg"
-              width="30"
-              height="30"
-              fill="currentColor"
-              viewBox="0 0 64 64"
-              style={{ margin: "10px", marginLeft: "5px" }}
-            >
-              <circle cx="32" cy="32" r="30" fill="none" stroke="#999" stroke-width="2"/>
-              <circle cx="32" cy="20" r="12" fill="#ccc" stroke="#999" stroke-width="2"/>
-              <path d="M16 52c0-8.8 7.2-16 16-16s16 7.2 16 16v4H16v-4z" fill="#ccc" stroke="#999" stroke-width="2"/>
-            </svg>
-          
-          <textarea
-            value={props.value.metadata.comment}
-            onChange={(e) => props.utils.setMetadata({ comment: e.target.value })}
-            placeholder="Enter your comment here..."
-            className="textarea"
-            style={{
-              ...commonTextStyle,
-              width: "calc(100% - 22px)",
-              height: "80px",
-              padding: "4px",
-              border: "none", //"1px solid #ccc",
-              // borderRadius: "4px",
-              backgroundColor: "transparent",
-              lineHeight: "16px",
-              fontSize: "12px",
-            }}
-            />
-          </div>
-          {/* reply button */}
-          <div style={{ display: 'flex', gap: '5px', alignItems: 'center', marginLeft: '40px' }}>
-            ⤷
-            <div style={{ fontSize: '12px' }}>Reply</div>
-          </div>
-          {/* <div style={{ marginTop: "10px" }}>
+        <textarea
+          value={props.value.metadata.comment}
+          onChange={(e) => props.utils.setMetadata({ comment: e.target.value })}
+          placeholder="Enter your comment here..."
+          className="textarea"
+          style={{
+            ...commonTextStyle,
+            width: "calc(100% - 22px)",
+            height: "80px",
+            padding: "4px",
+            border: "none", //"1px solid #ccc",
+            // borderRadius: "4px",
+            backgroundColor: "transparent",
+            lineHeight: "16px",
+            fontSize: "12px",
+          }}
+        />
+      </div>
+      {/* reply button */}
+      <div style={{ display: "flex", gap: "5px", alignItems: "center", marginLeft: "40px" }}>
+        ⤷<div style={{ fontSize: "12px" }}>Reply</div>
+      </div>
+      {/* <div style={{ marginTop: "10px" }}>
             <strong style={{ color: "#525252" }}>Replies:</strong>
             {replies.map((reply, index) => (
               <div
@@ -152,309 +170,70 @@
               Add Reply
             </button>
           </div> */}
-        </div>
-      );
-    };
+    </div>
+  );
+};
 
-    const ImageUpload: React.FC<AnnotationEditorProps> = (props) => {
-      const handleImageUpload = (e: React.ChangeEvent<HTMLInputElement>) => {
-        if (e.target.files && e.target.files[0]) {
-          const reader = new FileReader();
-          reader.onload = (event) => {
-            if (event.target && event.target.result) {
-              props.utils.setMetadata({ image: event.target.result as string });
-            }
-          };
-          reader.readAsDataURL(e.target.files[0]);
+const ImageUpload: React.FC<AnnotationEditorProps> = (props) => {
+  const handleImageUpload = (e: React.ChangeEvent<HTMLInputElement>) => {
+    if (e.target.files && e.target.files[0]) {
+      const reader = new FileReader();
+      reader.onload = (event) => {
+        if (event.target && event.target.result) {
+          props.utils.setMetadata({ image: event.target.result as string });
         }
       };
+      reader.readAsDataURL(e.target.files[0]);
+    }
+  };
 
-      return (
-        <div>
-          <input type="file" accept="image/*" onChange={handleImageUpload} style={commonTextStyle} />
-          {props.value.metadata.image && <img src={props.value.metadata.image} alt="Uploaded" />}
+  return (
+    <div>
+      <input type="file" accept="image/*" onChange={handleImageUpload} style={commonTextStyle} />
+      {props.value.metadata.image && (
+        <div
+          style={{
+            width: "320px",
+            height: "220px",
+            resize: "both",
+            overflow: "auto",
+            border: "1px solid #ccc",
+            marginTop: "8px",
+          }}>
+          <img
+            src={props.value.metadata.image}
+            alt="Uploaded"
+            style={{ width: "100%", height: "100%", objectFit: "contain", display: "block" }}
+          />
         </div>
-      );
-    };
-
-    const DisplayHTML: React.FC<AnnotationEditorProps> = (props) => {
-      const [htmlContent, setHtmlContent] = useState(props.value.metadata.html || 
-        //get text
-        props.utils.getText() || ""
-      );
-
-      const handleChange: React.ChangeEventHandler<HTMLTextAreaElement> = (e) => {
-        const newHtmlContent = e.target.value;
-        setHtmlContent(newHtmlContent);
-        props.utils.setMetadata({ html: newHtmlContent });
-      };
-
-      return (
-        <div>
-          {/* <textarea
-            value={htmlContent}
-            onChange={handleChange}
-            placeholder="Write your HTML code here"
-            style={{ ...commonTextStyle, width: "100%", height: "150px" }}
-          /> */}
-          <div dangerouslySetInnerHTML={{ __html: htmlContent }} style={{ height: '50px', resize: 'both', overflow: 'auto', border: "1px solid #ccc", }} />
-        </div >
-      );
-    };
-
-    const RunCodeSegment: React.FC<AnnotationEditorProps> = (props) => {
-      const [apiResName, setApiResName] = useState<string>(props.value.metadata.apiResName || "");
-      const [apiRes, setApiRes] = useState<string>(props.value.metadata.apiRes || "");
-      const [code, setCode] = useState<string[]>(props.value.metadata.code || ["", "", ""]);
-      const [pinBody, setPinBody] = useState<boolean>(props.value.metadata.pinBody || false);
-      const [showHead, setShowHead] = useState<boolean>(props.value.metadata.showHead || false);
-      const [showTail, setShowTail] = useState<boolean>(props.value.metadata.showTail || false);
-
-      function addReturn(code: string): string {
-        const lines = code.trim().split("\n");
-        if (lines.length === 0) {
-          return "";
-        }
-        const lastLine = lines[lines.length - 1];
-        lines[lines.length - 1] = `return ${lastLine.trim()}`;
-        return lines.join("\n");
-      }
-
-      async function runAndUpdateCode(): Promise<void> {
-        try {
-          let empty = true;
-          for (let i = 0; i < code.length; i++) {
-            if (String(code[i]).trim() !== "") {
-              empty = false;
-              break;
-            }
-          }
-          if (apiRes !== "" && apiResName === "") {
-            empty = false;
-          }
-          if (empty) {
-            props.utils.setMetadata({
-              error: "No code to run",
-              response: undefined,
-              code: code,
-            });
-            return;
-          }
-
-          let joinedCode = code.join("\n");
-          if (apiRes !== "" && apiResName !== "") {
-            joinedCode = `const ${apiResName} = Promise.resolve(${apiRes});\n${joinedCode}`;
-          }
-
-          const asyncFunction = new Function(`return (async () => { ${joinedCode} })();`);
-          let result = await asyncFunction();
-
-          if (result === undefined) {
-            const newCode = addReturn(joinedCode);
-            try {
-              const asyncReturnFunction = new Function(`return (async () => { ${newCode} })();`);
-              result = await asyncReturnFunction();
-            } catch {}
-          }
-
-          props.utils.setMetadata({
-            response: result || "Undefined",
-            error: undefined,
-            code,
-            apiRes,
-            apiResName,
-          });
-        } catch (e) {
-          props.utils.setMetadata({
-            response: undefined,
-            error: e instanceof Error ? e.message : String(e),
-            code,
-            apiRes,
-            apiResName,
-          });
-        }
-      }
+      )}
+    </div>
+  );
+};
 
-      return (
-        <div style={{ marginBottom: "10px" }}>
-          
-          <div style={{ marginBottom: "10px" }}>
-            <label style={commonTextStyle}>
-              <strong>Cached API Response</strong>
-            </label>
-            <div style={{ marginBottom: "10px" }}>
-              <label style={commonTextStyle}>Mock Response:</label>
-              <br></br>
-              <textarea
-                rows={4}
-                value={apiRes}
-                placeholder="Enter a JavaScript object..."
-                onChange={(e) => setApiRes(e.target.value)}
-                style={{
-                  ...commonTextStyle,
-                  width: "-webkit-fill-available",
-                  padding: "5px",
-                  border: "1px solid #ccc",
-                  borderRadius: "4px",
-                }}
-              />
-            </div>
-            <div style={{ marginBottom: "10px" }}>
-              <label style={commonTextStyle}>Mock Response Variable Name:</label>
-              <br />
-              <input
-                value={apiResName}
-                placeholder="Enter a variable name..."
-                onChange={(e) => setApiResName(e.target.value)}
-                style={{
-                  ...commonTextStyle,
-                  marginBottom: "10px",
-                  width: "-webkit-fill-available",
-                  padding: "5px",
-                  border: "1px solid #ccc",
-                  borderRadius: "4px",
-                }}
-              />
-            </div>
-            <div style={{ marginBottom: "10px" }}>
-              <label style={commonTextStyle}>Head:</label>
-              <br></br>
-              <textarea
-                rows={4}
-                value={code[0]}
-                placeholder="Enter other JS preprocessing code..."
-                onChange={(e) => {
-                  const newCode = [...code];
-                  newCode[0] = e.target.value;
-                  setCode(newCode);
-                }}
-                style={{
-                  ...commonTextStyle,
-                  width: "-webkit-fill-available",
-                  marginBottom: "10px",
-                  padding: "5px",
-                  border: "1px solid #ccc",
-                  borderRadius: "4px",
-                }}
-              />
-            </div>
-            <div style={{ marginBottom: "10px" }}>
-              <label style={commonTextStyle}>Body:</label>
-              <br></br>
-              <textarea
-                rows={4}
-                placeholder="Enter a JavaScript expression..."
-                value={pinBody ? props.utils.getText() : code[1]}
-                onChange={(e) => {
-                  if (!pinBody) {
-                    const newCode = [...code];
-                    newCode[1] = e.target.value;
-                    setCode(newCode);
-                  }
-                }}
-                style={{
-                  ...commonTextStyle,
-                  width: "-webkit-fill-available",
-                  padding: "5px",
-                  border: "1px solid #ccc",
-                  borderRadius: "4px",
-                }}
-              />
-              <div>
-                <label style={commonTextStyle}>
-                  <input
-                    type="checkbox"
-                    checked={pinBody}
-                    onChange={() => {
-                      setPinBody(!pinBody);
-                      props.utils.setMetadata({ pinBody: !pinBody });
-                    }}
-                  />
-                  Pin body to annotated document text
-                </label>
-              </div>
-            </div>
-            <div style={{ marginBottom: "10px" }}>
-              <label style={commonTextStyle}>Tail:</label>
-              <br></br>
-              <textarea
-                rows={4}
-                placeholder="Enter other JS postprocessing code..."
-                value={code[2]}
-                onChange={(e) => {
-                  const newCode = [...code];
-                  newCode[2] = e.target.value;
-                  setCode(newCode);
-                }}
-                style={{
-                  ...commonTextStyle,
-                  width: "-webkit-fill-available",
-                  marginBottom: "10px",
-                  padding: "5px",
-                  border: "1px solid #ccc",
-                  borderRadius: "4px",
-                }}
-              />
-            </div>
-          </div>
-          {props.value.metadata.error && (
-            <div style={{ color: "red", marginBottom: "10px", ...commonTextStyle }}>
-              An error occurred: {props.value.metadata.error}
-            </div>
-          )}
-          {props.value.metadata.response && (
-            <div style={{ marginBottom: "10px", ...commonTextStyle }}>
-              <strong>Response:</strong> <ObjectInspector data={props.value.metadata.response} />
-            </div>
-          )}
-          <div style={{ marginBottom: "10px" }}>
-            <button
-              onClick={runAndUpdateCode}
-              style={{
-                marginRight: "10px",
-                ...commonTextStyle,
-                padding: "5px 10px",
-                border: "1px solid #ccc",
-                borderRadius: "4px",
-                cursor: "pointer",
-              }}>
-              Run Code
-            </button>
-            { props.value.metadata.response
-            && <button
-                onClick={() =>
-                  props.utils.setMetadata({
-                    response: undefined,
-                    error: undefined,
-                  })
-                }
-                style={{
-                  ...commonTextStyle,
-                  padding: "5px 10px",
-                  border: "1px solid #ccc",
-                  borderRadius: "4px",
-                  cursor: "pointer",
-                }}>
-                Clear Output
-              </button>
-            }
-          </div>
-        </div>
-      );
-    };
+const DisplayHTML: React.FC<AnnotationEditorProps> = (props) => {
+  return (
+    <div>
+      <div
+        dangerouslySetInnerHTML={{ __html: props.utils.getText() }}
+        style={{ height: "50px", resize: "both", overflow: "auto", border: "1px solid #ccc" }}
+      />
+    </div>
+  );
+};
 
-    const Odyssey: React.FC<AnnotationEditorProps> = (props) => {
-      const [expression, setExpression] = useState(props.value.metadata.expression || "loading...");
-      const [retryParse, setRetryParse] = useState(false);
+const Odyssey: React.FC<AnnotationEditorProps> = (props) => {
+  const [expression, setExpression] = useState(props.value.metadata.expression || "loading...");
+  const [retryParse, setRetryParse] = useState(false);
 
-      useEffect(() => {
-        // Only make API call if expression is "loading..." or retry was clicked
-        if (expression === "loading..." || retryParse) {
-          const parseText = async (text: string) => {
-            const prompt: ChatMessage[] = [
-              {
-                role: "system",
-                content: `Can you parse this piece of text or code to find an expression 
+  useEffect(() => {
+    // Only make API call if expression is "loading..." or retry was clicked
+    if (expression === "loading..." || retryParse) {
+      const parseText = async (text: string) => {
+        const prompt: ChatMessage[] = [
+          {
+            role: "system",
+            content: `Can you parse this piece of text or code to find an expression 
                   and convert it to mathjs parsable syntax? All math.h operators are allowed. 
                   If a term of the expression can be written with simple mathematical operators,
                   use those instead of 'function' like operators, for example, use 'x^y' instead of
@@ -465,2059 +244,93 @@
                   
                   The text to parse is as follows:
                   ${text}
-                `
-              }
-            ]
-            const parsed = await lmApi.chat(prompt, {
-              vendor: 'copilot',
-              family: 'gpt-4o',
-              temperature: 0.3
-            })
-        
-            const newExpression = parsed;
-            setExpression(newExpression);
-            // Store in metadata for persistence
-            props.utils.setMetadata({ expression: newExpression });
-            setRetryParse(false);
-          }
-
-          parseText(props.utils.getText());
-        }
-      }, [props.utils, retryParse]);
-
-      // Update metadata when user manually edits the expression
-      const handleExpressionChange = (evt: React.ChangeEvent<HTMLInputElement>) => {
-        const newExpression = evt.target.value;
-        setExpression(newExpression);
-        props.utils.setMetadata({ expression: newExpression });
-      };
-
-      const odysseyBase = "https://herbie-fp.github.io/odyssey/?spec="
-      const url = odysseyBase + encodeURIComponent(expression);
-
-      return (
-        <div className="odyssey">
-          <p>Parsed the following expression from highlighted text:</p>
-          <input type="text" className="odyssey-text"
-            onChange={handleExpressionChange} value={expression}/>
-          <button onClick={() => setRetryParse(true)}>Retry</button>
-          <p>
-            Explore floating-point error in this expression with
-            <button className="open-external" onClick={() => vscode.postMessage({command: "open-external", url})}>
-              Odyssey 
-              <svg className="open-external-icon" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 256 256"><path d="M224,104a8,8,0,0,1-16,0V59.32l-66.33,66.34a8,8,0,0,1-11.32-11.32L196.68,48H152a8,8,0,0,1,0-16h64a8,8,0,0,1,8,8Zm-40,24a8,8,0,0,0-8,8v72H48V80h72a8,8,0,0,0,0-16H48A16,16,0,0,0,32,80V208a16,16,0,0,0,16,16H176a16,16,0,0,0,16-16V136A8,8,0,0,0,184,128Z"></path></svg>
-            </button>
-          </p>
-        </div>
-      );
-    };
-
-    /* TODO: Define additional tools as React components here. */
-    const ExplainInEnglish: React.FC<AnnotationEditorProps> = (props) => {
-      // State management for explanations
-      const [explanations, setExplanations] = useState({
-        what: props.value.metadata.whatExplanation || '',
-        how: props.value.metadata.howExplanation || '',
-        context: props.value.metadata.contextExplanation || '',
-        why: props.value.metadata.whyExplanation || ''
-      });
-      
-      const [presentationSummary, setPresentationSummary] = useState(
-        props.value.metadata.presentationSummary || ''
-      );
-      
-      const [explanationMode, setExplanationMode] = useState<'presentation' | 'in-depth'>(
-        props.value.metadata.explanationMode || 'presentation'
-      );
-      
-      const [isLoading, setIsLoading] = useState(false);
-      const [error, setError] = useState<string | null>(null);
-      const [executionResult, setExecutionResult] = useState<string | null>(
-        props.value.metadata.executionResult || null
-      );
-      const [executionError, setExecutionError] = useState<string | null>(
-        props.value.metadata.executionError || null
-      );
-      const [useMock, setUseMock] = useState(false);
-      const [isExecuting, setIsExecuting] = useState(false);
-      
-      // Track if component is mounted
-      const isMounted = useRef(true);
-
-      useEffect(() => {
-        return () => {
-          isMounted.current = false;
-        };
-      }, []);
-
-      // Get the highlighted code and document context
-      const highlightedCode = props.utils.getText();
-      const documentText = props.value.document || '';
-      const startPos = props.value.start;
-      const endPos = props.value.end;
-
-      // Save state changes to metadata
-      useEffect(() => {
-        props.utils.setMetadata({ 
-          whatExplanation: explanations.what,
-          howExplanation: explanations.how,
-          contextExplanation: explanations.context,
-          whyExplanation: explanations.why,
-          presentationSummary,
-          explanationMode,
-          executionResult,
-          executionError
-        });
-      }, [explanations, presentationSummary, explanationMode, executionResult, executionError]);
-
-      // Create formatted document with highlighted section
-      const createFormattedDocument = () => {
-        if (!documentText) {
-          return '';
-        }
-        
-        const before = documentText.substring(0, startPos);
-        const highlighted = documentText.substring(startPos, endPos);
-        const after = documentText.substring(endPos);
-        
-        return `${before}<<<HIGHLIGHTED>${highlighted}</HIGHLIGHTED>>>${after}`;
-      };
-
-      // Generate English explanation
-      const generateExplanation = async () => {
-        if (!highlightedCode.trim()) {
-          setError('No code selected to explain');
-          return;
-        }
-
-        setIsLoading(true);
-        setError(null);
-
-        try {
-          const formattedDocument = createFormattedDocument();
-          
-          const basePrompt = `You are a helpful assistant that explains JavaScript code in simple, clear English. 
-
-    You will be given a document with a highlighted section marked by <<<HIGHLIGHTED>...</HIGHLIGHTED>>> tags.
-
-    Please provide explanations for the highlighted code in four specific categories:
-
-    1. WHAT: What does this code do? (describe the main functionality and purpose)
-    2. HOW: How does this code work? (explain the technical implementation and logic flow)
-    3. CONTEXT: What is this code's function in the context of the entire class/component it belongs to? (explain its role in the larger system)
-    4. WHY: Why is this code needed? (explain the problem it solves and its importance)
-
-    Use clear, non-technical language that a beginner could understand. Focus on being concise but comprehensive.`;
-
-          if (explanationMode === 'presentation') {
-            const presentationPrompt: ChatMessage[] = [
-              { 
-                role: "system", 
-                content: `${basePrompt}
-
-    Format your response as a single cohesive explanation with bullet points for each category:
-
-    **What the code does:**
-    • [2-3 concise bullet points]
-
-    **How the code works:**
-    • [2-3 concise bullet points]
-
-    **Context within the class/component:**
-    • [2-3 concise bullet points]
-
-    **Why it's needed:**
-    • [2-3 concise bullet points]
-
-    Keep each bullet point to 1-2 sentences maximum. This should be easy to read without scrolling.`
-              },
-              { 
-                role: "user", 
-                content: `Here is the code with the highlighted section:\n\n${formattedDocument || highlightedCode}\n\n` +
-                        `Please explain the highlighted code in presentation format.`
-              }
-            ];
-
-            let response: string;
-            if (useMock) {
-              await new Promise(resolve => setTimeout(resolve, 1000));
-              response = `**What the code does:**
-    • Sets up state variables for managing user interface interactions
-    • Handles data processing and validation logic
-    • Manages component lifecycle and cleanup operations
-
-    **How the code works:**
-    • Uses React hooks to track component state changes
-    • Implements async functions for API communication
-    • Applies error handling with try-catch blocks
-
-    **Context within the class/component:**
-    • Serves as the core data processing logic for the component
-    • Integrates with other component methods for state management
-    • Provides essential functionality for user interactions
-
-    **Why it's needed:**
-    • Ensures proper data flow and state consistency
-    • Prevents memory leaks and handles edge cases
-    • Enables responsive user experience and error recovery`;
-            } else {
-              try {
-                response = await lmApi.chat(presentationPrompt, {
-                  vendor: 'copilot',
-                  family: 'gpt-4o',
-                  temperature: 0.7
-                });
-              } catch (apiError) {
-                console.log('API call failed, falling back to mock:', apiError);
-                response = `**What the code does:**
-    • Sets up state variables for managing user interface interactions
-    • Handles data processing and validation logic
-    • Manages component lifecycle and cleanup operations
-
-    **How the code works:**
-    • Uses React hooks to track component state changes
-    • Implements async functions for API communication
-    • Applies error handling with try-catch blocks
-
-    **Context within the class/component:**
-    • Serves as the core data processing logic for the component
-    • Integrates with other component methods for state management
-    • Provides essential functionality for user interactions
-
-    **Why it's needed:**
-    • Ensures proper data flow and state consistency
-    • Prevents memory leaks and handles edge cases
-    • Enables responsive user experience and error recovery`;
-              }
-            }
-
-            if (isMounted.current) {
-              setPresentationSummary(response);
-            }
-          } else {
-            // In-depth mode - get detailed explanations for each category
-            const inDepthPrompt: ChatMessage[] = [
-              { 
-                role: "system", 
-                content: `${basePrompt}
-
-    You MUST respond with ONLY a valid JSON object. No additional text, explanations, or formatting outside the JSON.
-
-    The JSON should have exactly this structure:
-    {
-      "what": "Detailed explanation of what the code does (3-5 sentences)...",
-      "how": "Detailed explanation of how it works technically (3-5 sentences)...",
-      "context": "Detailed explanation of its role in the larger system (3-5 sentences)...",
-      "why": "Detailed explanation of why it's necessary (3-5 sentences)..."
-    }
-
-    Each value should be a single string with 3-5 sentences. Do not include any markdown, formatting, or line breaks within the strings.`
-              },
-              { 
-                role: "user", 
-                content: `Here is the code with the highlighted section:\n\n${formattedDocument || highlightedCode}\n\n` +
-                        `Please provide detailed explanations for each category in JSON format.`
-              }
-            ];
-
-            let response: string;
-            if (useMock) {
-              await new Promise(resolve => setTimeout(resolve, 1000));
-              response = JSON.stringify({
-                what: "This code defines state management and UI interaction logic for a React component. It establishes multiple state variables using the useState hook to track different aspects of the component's behavior, including user inputs, loading states, error conditions, and execution results. The code also sets up effect hooks to handle component lifecycle events and data persistence.\n\nThe primary function is to create a controlled interface that responds to user actions while maintaining data integrity. It manages both the visual presentation of information and the underlying data processing that supports the component's functionality.\n\nAdditionally, this code implements proper cleanup mechanisms to prevent memory leaks and ensures that asynchronous operations are handled correctly even when the component unmounts during execution.",
-                how: "The implementation uses React's built-in hooks pattern to manage state and side effects. The useState hooks create reactive state variables that automatically trigger re-renders when their values change. Each state variable serves a specific purpose and is updated through setter functions that maintain immutability principles.\n\nThe useEffect hooks create a dependency tracking system that automatically runs cleanup or update logic when specific values change. This creates a reactive programming model where changes in one part of the system automatically propagate to other dependent parts.\n\nThe code also implements proper error boundary patterns using try-catch blocks and loading states, ensuring that the user interface remains responsive and informative even when operations fail or take time to complete.",
-                context: "Within the larger component architecture, this code serves as the foundational state management layer that all other component methods depend on. It acts as the single source of truth for the component's current status and provides the reactive infrastructure that other functions can interact with.\n\nThis state management setup enables other parts of the component to perform operations like API calls, user input handling, and data validation while maintaining consistent state across the entire component lifecycle. It integrates with the component's rendering logic to ensure that UI changes reflect the current application state.\n\nThe code also establishes the communication patterns between this component and its parent components or global state management systems, ensuring that data flows correctly throughout the application hierarchy.",
-                why: "This state management structure is essential for creating a reliable and user-friendly interface. Without proper state tracking, the component would not be able to provide visual feedback to users about loading states, errors, or successful operations, leading to a poor user experience.\n\nThe structured approach to state management prevents common React pitfalls like state inconsistencies, memory leaks from unmounted components, and race conditions from asynchronous operations. This defensive programming approach ensures the component remains stable even under adverse conditions.\n\nFurthermore, this pattern establishes a maintainable codebase where future developers can easily understand and modify the component's behavior. The clear separation of concerns and consistent naming conventions make the code self-documenting and reduce the likelihood of bugs during maintenance or feature additions."
-              });
-            } else {
-              try {
-                response = await lmApi.chat(inDepthPrompt, {
-                  vendor: 'copilot',
-                  family: 'gpt-4o',
-                  temperature: 0.7
-                });
-              } catch (apiError) {
-                console.log('API call failed, falling back to mock:', apiError);
-                response = JSON.stringify({
-                  what: "This code defines state management and UI interaction logic for a React component. It establishes multiple state variables using the useState hook to track different aspects of the component's behavior, including user inputs, loading states, error conditions, and execution results. The code also sets up effect hooks to handle component lifecycle events and data persistence.",
-                  how: "The implementation uses React's built-in hooks pattern to manage state and side effects. The useState hooks create reactive state variables that automatically trigger re-renders when their values change. Each state variable serves a specific purpose and is updated through setter functions that maintain immutability principles.",
-                  context: "Within the larger component architecture, this code serves as the foundational state management layer that all other component methods depend on. It acts as the single source of truth for the component's current status and provides the reactive infrastructure that other functions can interact with.",
-                  why: "This state management structure is essential for creating a reliable and user-friendly interface. Without proper state tracking, the component would not be able to provide visual feedback to users about loading states, errors, or successful operations, leading to a poor user experience."
-                });
-              }
-            }
-
-            try {
-              // Try to parse as JSON first
-              const parsedResponse = JSON.parse(response);
-              if (isMounted.current) {
-                setExplanations({
-                  what: parsedResponse.what || '',
-                  how: parsedResponse.how || '',
-                  context: parsedResponse.context || '',
-                  why: parsedResponse.why || ''
-                });
-              }
-            } catch (parseError) {
-              // If JSON parsing fails, try to extract content between JSON markers or use fallback
-              console.log('JSON parsing failed, attempting to extract or use fallback:', parseError);
-              
-              try {
-                // Try to find JSON content within the response
-                const jsonMatch = response.match(/\{[\s\S]*\}/);
-                if (jsonMatch) {
-                  const parsedResponse = JSON.parse(jsonMatch[0]);
-                  if (isMounted.current) {
-                    setExplanations({
-                      what: parsedResponse.what || '',
-                      how: parsedResponse.how || '',
-                      context: parsedResponse.context || '',
-                      why: parsedResponse.why || ''
-                    });
-                  }
-                } else {
-                  // Fallback: treat the response as a single explanation and distribute it
-                  const fallbackText = response.trim();
-                  const sections = fallbackText.split(/(?:\n\s*){2,}/); // Split on double line breaks
-                  
-                  if (isMounted.current) {
-                    setExplanations({
-                      what: sections[0] || fallbackText,
-                      how: sections[1] || 'Technical implementation details for the highlighted code.',
-                      context: sections[2] || 'This code functions as part of the larger component/class structure.',
-                      why: sections[3] || 'This code is necessary to ensure proper functionality and user experience.'
-                    });
-                  }
-                }
-              } catch (secondParseError) {
-                console.log('All parsing attempts failed, using basic fallback');
-                if (isMounted.current) {
-                  setExplanations({
-                    what: response || 'Unable to generate explanation',
-                    how: 'Technical implementation could not be parsed from the response.',
-                    context: 'Context information could not be extracted.',
-                    why: 'Reasoning could not be determined from the response.'
-                  });
-                }
-              }
-            }
-          }
-        } catch (err) {
-          const errorMsg = err instanceof Error ? err.message : 'An error occurred while generating explanation';
-          
-          if (isMounted.current) {
-            setError(errorMsg);
-          }
-        } finally {
-          if (isMounted.current) {
-            setIsLoading(false);
-          }
-        }
-      };
-
-      // Execute the highlighted code (keeping original logic)
-      const executeCode = async () => {
-        setIsExecuting(true);
-        setExecutionError(null);
-        setExecutionResult(null);
-
-        try {
-          const code = highlightedCode.trim();
-          let result;
-          
-          try {
-            const asyncFunction = new Function(`
-              'use strict';
-              return (async () => {
-                ${code}
-              })();
-            `);
-            result = await asyncFunction();
-          } catch (firstError) {
-            const lines = code.split('\n');
-            if (lines.length > 0) {
-              const lastLine = lines[lines.length - 1].trim();
-              if (!lastLine.startsWith('return') && !lastLine.startsWith('throw')) {
-                lines[lines.length - 1] = `return ${lastLine}`;
-                const modifiedCode = lines.join('\n');
-                
-                try {
-                  const asyncFunction = new Function(`
-                    'use strict';
-                    return (async () => {
-                      ${modifiedCode}
-                    })();
-                  `);
-                  result = await asyncFunction();
-                } catch (secondError) {
-                  throw firstError;
-                }
-              } else {
-                throw firstError;
-              }
-            } else {
-              throw firstError;
-            }
-          }
-
-          if (result === undefined) {
-            setExecutionResult('undefined');
-          } else if (result === null) {
-            setExecutionResult('null');
-          } else if (typeof result === 'object') {
-            setExecutionResult(JSON.stringify(result, null, 2));
-          } else {
-            setExecutionResult(String(result));
-          }
-        } catch (err) {
-          setExecutionError(err instanceof Error ? err.message : String(err));
-        } finally {
-          setIsExecuting(false);
-        }
-      };
-
-      return (
-        <div style={{ 
-          padding: "12px", 
-          fontFamily: "Poppins, -apple-system, BlinkMacSystemFont, sans-serif",
-          fontSize: "14px",
-          maxWidth: "100%"
-        }}>
-          <div style={{ marginBottom: "16px" }}>
-            <h3 style={{ 
-              margin: "0 0 12px 0", 
-              fontSize: "16px", 
-              fontWeight: "600",
-              color: "#333"
-            }}>
-              Code Explanation in Plain English
-            </h3>
-            
-            <div style={{ 
-              display: "flex", 
-              gap: "10px", 
-              alignItems: "center",
-              marginBottom: "12px",
-              flexWrap: "wrap"
-            }}>
-              <button
-                onClick={generateExplanation}
-                disabled={isLoading}
-                style={{
-                  padding: "8px 16px",
-                  backgroundColor: isLoading ? "#e0e0e0" : "#0078D4",
-                  color: "white",
-                  border: "none",
-                  borderRadius: "4px",
-                  cursor: isLoading ? "not-allowed" : "pointer",
-                  fontSize: "14px",
-                  fontWeight: "500",
-                  transition: "background-color 0.2s"
-                }}
-              >
-                {isLoading ? "Generating..." : "Generate Explanation"}
-              </button>
-              
-              <div style={{ display: "flex", alignItems: "center", gap: "8px" }}>
-                <label style={{ fontSize: "13px", color: "#666", fontWeight: "500" }}>
-                  Mode:
-                </label>
-                <select
-                  value={explanationMode}
-                  onChange={(e) => setExplanationMode(e.target.value as 'presentation' | 'in-depth')}
-                  style={{
-                    padding: "6px 10px",
-                    borderRadius: "4px",
-                    border: "1px solid #ccc",
-                    fontSize: "13px",
-                    backgroundColor: "white"
-                  }}
-                >
-                  <option value="presentation">Presentation (Summary)</option>
-                  <option value="in-depth">In-Depth (Detailed)</option>
-                </select>
-              </div>
-              
-              <label style={{ 
-                display: "flex", 
-                alignItems: "center", 
-                fontSize: "13px",
-                cursor: "pointer",
-                color: "#666"
-              }}>
-                <input 
-                  type="checkbox"
-                  checked={useMock}
-                  onChange={() => setUseMock(!useMock)}
-                  style={{ marginRight: "6px" }}
-                />
-                Use mock API
-              </label>
-            </div>
-
-            {error && (
-              <div style={{ 
-                color: "#D83B01", 
-                backgroundColor: "#FFF4F2", 
-                padding: "10px", 
-                borderRadius: "4px",
-                marginBottom: "12px",
-                fontSize: "13px",
-                border: "1px solid #FDBCB4"
-              }}>
-                ⚠️ {error}
-              </div>
-            )}
-
-            {explanationMode === 'presentation' ? (
-              <div style={{ marginBottom: "16px" }}>
-                <label style={{ 
-                  display: "block", 
-                  marginBottom: "8px", 
-                  fontWeight: "600",
-                  fontSize: "14px",
-                  color: "#444"
-                }}>
-                  Code Explanation Summary:
-                </label>
-                <textarea
-                  value={presentationSummary}
-                  onChange={(e) => setPresentationSummary(e.target.value)}
-                  placeholder="Click 'Generate Explanation' to get a concise summary with bullet points for What, How, Context, and Why..."
-                  style={{
-                    width: "100%",
-                    minHeight: "200px",
-                    padding: "12px",
-                    borderRadius: "4px",
-                    border: "1px solid #ccc",
-                    fontSize: "14px",
-                    lineHeight: "1.6",
-                    resize: "vertical",
-                    fontFamily: "inherit",
-                    backgroundColor: "#FAFAFA"
-                  }}
-                />
-              </div>
-            ) : (
-              <div style={{ marginBottom: "16px" }}>
-                {[
-                  { key: 'what', title: 'What does this code do?', color: '#E3F2FD' },
-                  { key: 'how', title: 'How does this code work?', color: '#F3E5F5' },
-                  { key: 'context', title: 'Context within the class/component', color: '#E8F5E8' },
-                  { key: 'why', title: 'Why is this code needed?', color: '#FFF3E0' }
-                ].map(({ key, title, color }) => (
-                  <div key={key} style={{ marginBottom: "16px" }}>
-                    <label style={{ 
-                      display: "block", 
-                      marginBottom: "8px", 
-                      fontWeight: "600",
-                      fontSize: "14px",
-                      color: "#444"
-                    }}>
-                      {title}
-                    </label>
-                    <textarea
-                      value={explanations[key as keyof typeof explanations]}
-                      onChange={(e) => setExplanations(prev => ({ ...prev, [key]: e.target.value }))}
-                      placeholder={`Detailed explanation of ${key}...`}
-                      style={{
-                        width: "100%",
-                        minHeight: "120px",
-                        padding: "12px",
-                        borderRadius: "4px",
-                        border: "1px solid #ccc",
-                        fontSize: "14px",
-                        lineHeight: "1.6",
-                        resize: "vertical",
-                        fontFamily: "inherit",
-                        backgroundColor: color
-                      }}
-                    />
-                  </div>
-                ))}
-              </div>
-            )}
-
-            <div style={{ 
-              borderTop: "1px solid #E1E1E1",
-              paddingTop: "16px",
-              marginTop: "16px"
-            }}>
-              <h4 style={{ 
-                margin: "0 0 12px 0", 
-                fontSize: "15px", 
-                fontWeight: "600",
-                color: "#333"
-              }}>
-                Code Execution
-              </h4>
-              
-              <button
-                onClick={executeCode}
-                disabled={isExecuting || !highlightedCode.trim()}
-                style={{
-                  padding: "8px 16px",
-                  backgroundColor: isExecuting ? "#e0e0e0" : "#107C10",
-                  color: "white",
-                  border: "none",
-                  borderRadius: "4px",
-                  cursor: (isExecuting || !highlightedCode.trim()) ? "not-allowed" : "pointer",
-                  fontSize: "14px",
-                  fontWeight: "500",
-                  marginBottom: "12px",
-                  transition: "background-color 0.2s"
-                }}
-              >
-                {isExecuting ? "Executing..." : "▶ Execute Code"}
-              </button>
-
-              {executionResult !== null && (
-                <div style={{ 
-                  backgroundColor: "#F0FFF4",
-                  border: "1px solid #B7EB8F",
-                  borderRadius: "4px",
-                  padding: "12px",
-                  marginTop: "12px"
-                }}>
-                  <div style={{ 
-                    fontWeight: "600", 
-                    marginBottom: "8px",
-                    color: "#52C41A",
-                    fontSize: "13px"
-                  }}>
-                    ✓ Execution Result:
-                  </div>
-                  <pre style={{ 
-                    margin: 0,
-                    fontFamily: "Consolas, Monaco, 'Courier New', monospace",
-                    fontSize: "13px",
-                    whiteSpace: "pre-wrap",
-                    wordBreak: "break-word",
-                    color: "#333",
-                    backgroundColor: "white",
-                    padding: "8px",
-                    borderRadius: "3px"
-                  }}>
-                    {executionResult}
-                  </pre>
-                </div>
-              )}
-
-              {executionError && (
-                <div style={{ 
-                  backgroundColor: "#FFF2F0",
-                  border: "1px solid #FFCCC7",
-                  borderRadius: "4px",
-                  padding: "12px",
-                  marginTop: "12px"
-                }}>
-                  <div style={{ 
-                    fontWeight: "600", 
-                    marginBottom: "8px",
-                    color: "#FF4D4F",
-                    fontSize: "13px"
-                  }}>
-                    ✗ Execution Error:
-                  </div>
-                  <pre style={{ 
-                    margin: 0,
-                    fontFamily: "Consolas, Monaco, 'Courier New', monospace",
-                    fontSize: "13px",
-                    whiteSpace: "pre-wrap",
-                    wordBreak: "break-word",
-                    color: "#8B0000",
-                    backgroundColor: "white",
-                    padding: "8px",
-                    borderRadius: "3px"
-                  }}>
-                    {executionError}
-                  </pre>
-                </div>
-              )}
-            </div>
-
-            <div style={{
-              marginTop: "16px",
-              padding: "10px",
-              backgroundColor: "#F5F5F5",
-              borderRadius: "4px",
-              fontSize: "12px",
-              color: "#666"
-            }}>
-              <strong>Highlighted Code:</strong>
-              <pre style={{
-                margin: "8px 0 0 0",
-                padding: "8px",
-                backgroundColor: "white",
-                borderRadius: "3px",
-                fontSize: "12px",
-                overflow: "auto",
-                border: "1px solid #E0E0E0"
-              }}>
-                {highlightedCode || "(No code selected)"}
-              </pre>
-            </div>
-          </div>
-        </div>
-      );
-    };
-
-    const OutputVisualizer: React.FC<AnnotationEditorProps> = (props) => {
-      const [predictedOutput, setPredictedOutput] = useState(
-        props.value.metadata.predictedOutput || ''
-      );
-      const [variableChanges, setVariableChanges] = useState(
-        props.value.metadata.variableChanges || []
-      );
-      const [llmExplanation, setLlmExplanation] = useState(
-        props.value.metadata.llmExplanation || ''
-      );
-      const [confidence, setConfidence] = useState(
-        props.value.metadata.confidence || 'medium'
-      );
-      const [isAnalyzing, setIsAnalyzing] = useState(false);
-      const [testInputs, setTestInputs] = useState(
-        props.value.metadata.testInputs || ''
-      );
-      const [actualOutput, setActualOutput] = useState(
-        props.value.metadata.actualOutput || null
-      );
-      const [executionError, setExecutionError] = useState(
-        props.value.metadata.executionError || null
-      );
-
-      // Get the highlighted code and document context
-      const highlightedCode = props.utils.getText();
-      const documentText = props.value.document || '';
-
-      // Save state to metadata
-      useEffect(() => {
-        props.utils.setMetadata({
-          predictedOutput,
-          variableChanges,
-          llmExplanation,
-          confidence,
-          testInputs,
-          actualOutput,
-          executionError
-        });
-      }, [predictedOutput, variableChanges, llmExplanation, confidence, testInputs, actualOutput, executionError]);
-
-      // Analyze code and predict output
-      const analyzeCode = async () => {
-        setIsAnalyzing(true);
-        
-        // Simulate analysis (in real implementation, this would call an LLM API)
-        setTimeout(() => {
-          const code = highlightedCode.trim();
-          
-          // Check if it's the quickSort function
-          if (code.includes('quickSort') && code.includes('partition')) {
-            setPredictedOutput('A sorted version of the input array \'arr\'');
-            setVariableChanges([
-              {
-                variable: 'arr',
-                before: 'The input array passed to quickSort',
-                after: 'The sorted version of the input array'
-              }
-            ]);
-            setLlmExplanation('The highlighted \'quickSort\' function sorts the input array \'arr\' in-place using the partitioning logic defined in the \'partition\' function. The \'arr\' variable is modified directly during the sorting process.');
-            setConfidence('high');
-          }
-          // Check if it's the partition function
-          else if (code.includes('partition') && code.includes('pivot')) {
-            setPredictedOutput('The index position where the pivot element is placed after partitioning');
-            setVariableChanges([
-              {
-                variable: 'arr',
-                before: 'The array segment between low and high indices',
-                after: 'Rearranged with elements less than pivot on left, greater on right'
-              },
-              {
-                variable: 'i',
-                before: 'Initialized to low - 1',
-                after: 'Final position before the pivot'
-              }
-            ]);
-            setLlmExplanation('The \'partition\' function rearranges the array segment between \'low\' and \'high\' indices, using the last element as a pivot. It returns the final position of the pivot after partitioning.');
-            setConfidence('high');
-          }
-          // Generic function detection
-          else if (code.includes('function') || code.includes('=>')) {
-            setPredictedOutput('Function output depends on input parameters');
-            setVariableChanges([]);
-            setLlmExplanation('This appears to be a function definition. The actual output will depend on the input parameters provided when the function is called.');
-            setConfidence('low');
-          }
-          // Default case
-          else {
-            setPredictedOutput('Code execution result');
-            setVariableChanges([]);
-            setLlmExplanation('The highlighted code performs operations. Specific output depends on the context and any variables it uses.');
-            setConfidence('low');
-          }
-          
-          setIsAnalyzing(false);
-        }, 1000);
-      };
-
-      // Execute code with test inputs
-      const executeCode = async () => {
-        if (!testInputs.trim()) {
-          setExecutionError('Please provide test inputs to execute the function');
-          return;
-        }
-
-        try {
-          const code = highlightedCode.trim();
-          let executionCode = code;
-          
-          // Detect if it's a function and create test call
-          const functionMatch = code.match(/function\s+(\w+)/);
-          if (functionMatch) {
-            executionCode = `${code}\n\n${functionMatch[1]}(${testInputs})`;
-          }
-
-          const asyncFunction = new Function(`
-            'use strict';
-            return (async () => {
-              ${executionCode}
-            })();
-          `);
-          
-          const result = await asyncFunction();
-          
-          if (result === undefined) {
-            setActualOutput('undefined (no return value)');
-          } else if (result === null) {
-            setActualOutput('null');
-          } else if (typeof result === 'object') {
-            setActualOutput(JSON.stringify(result, null, 2));
-          } else {
-            setActualOutput(String(result));
-          }
-          setExecutionError(null);
-        } catch (err) {
-          setExecutionError(err instanceof Error ? err.message : String(err));
-          setActualOutput(null);
-        }
-      };
-
-      const getConfidenceColor = () => {
-        switch(confidence) {
-          case 'high': return '#22c55e';
-          case 'medium': return '#f59e0b';
-          case 'low': return '#ef4444';
-          default: return '#6b7280';
-        }
-      };
-
-      return (
-        <div style={{
-          fontFamily: "-apple-system, BlinkMacSystemFont, 'Segoe UI', Roboto, sans-serif",
-          fontSize: "14px",
-          lineHeight: "1.6",
-          color: "#1f2937"
-        }}>
-          {/* Predicted Output Section */}
-          <div style={{
-            backgroundColor: "#f9fafb",
-            padding: "16px",
-            borderRadius: "8px",
-            marginBottom: "16px"
-          }}>
-            <div style={{
-              fontWeight: "600",
-              marginBottom: "8px",
-              fontSize: "15px"
-            }}>
-              Predicted return / output:
-            </div>
-            <div style={{
-              backgroundColor: "white",
-              padding: "12px",
-              borderRadius: "6px",
-              border: "1px solid #e5e7eb"
-            }}>
-              {predictedOutput || 
-                <span style={{ color: "#9ca3af", fontStyle: "italic" }}>
-                  Click "Analyze Code" to predict output
-                </span>
-              }
-            </div>
-          </div>
-
-          {/* Variable Changes Section */}
-          <div style={{
-            backgroundColor: "#f9fafb",
-            padding: "16px",
-            borderRadius: "8px",
-            marginBottom: "16px"
-          }}>
-            <div style={{
-              fontWeight: "600",
-              marginBottom: "12px",
-              fontSize: "15px"
-            }}>
-              Predicted variable changes:
-            </div>
-            {variableChanges.length > 0 ? (
-              <table style={{
-                width: "100%",
-                backgroundColor: "white",
-                borderRadius: "6px",
-                overflow: "hidden",
-                border: "1px solid #e5e7eb"
-              }}>
-                <thead>
-                  <tr style={{ backgroundColor: "#f3f4f6" }}>
-                    <th style={{
-                      padding: "10px",
-                      textAlign: "left",
-                      fontWeight: "600",
-                      borderBottom: "1px solid #e5e7eb",
-                      width: "20%"
-                    }}>
-                      Variable
-                    </th>
-                    <th style={{
-                      padding: "10px",
-                      textAlign: "left",
-                      fontWeight: "600",
-                      borderBottom: "1px solid #e5e7eb",
-                      width: "40%"
-                    }}>
-                      Before
-                    </th>
-                    <th style={{
-                      padding: "10px",
-                      textAlign: "left",
-                      fontWeight: "600",
-                      borderBottom: "1px solid #e5e7eb",
-                      width: "40%"
-                    }}>
-                      After
-                    </th>
-                  </tr>
-                </thead>
-                <tbody>
-                  {variableChanges.map((change: any, index: number) => (
-                    <tr key={index}>
-                      <td style={{
-                        padding: "10px",
-                        fontFamily: "monospace",
-                        fontSize: "13px",
-                        fontWeight: "500"
-                      }}>
-                        {change.variable}
-                      </td>
-                      <td style={{
-                        padding: "10px",
-                        fontSize: "13px",
-                        color: "#4b5563"
-                      }}>
-                        {change.before}
-                      </td>
-                      <td style={{
-                        padding: "10px",
-                        fontSize: "13px",
-                        color: "#4b5563"
-                      }}>
-                        {change.after}
-                      </td>
-                    </tr>
-                  ))}
-                </tbody>
-              </table>
-            ) : (
-              <div style={{
-                backgroundColor: "white",
-                padding: "12px",
-                borderRadius: "6px",
-                border: "1px solid #e5e7eb",
-                color: "#9ca3af",
-                fontStyle: "italic"
-              }}>
-                No variable changes predicted
-              </div>
-            )}
-          </div>
-
-          {/* LLM Explanation Section */}
-          <div style={{
-            backgroundColor: "#f9fafb",
-            padding: "16px",
-            borderRadius: "8px",
-            marginBottom: "16px"
-          }}>
-            <div style={{
-              fontWeight: "600",
-              marginBottom: "8px",
-              fontSize: "15px"
-            }}>
-              LLM explanation:
-            </div>
-            <div style={{
-              backgroundColor: "white",
-              padding: "12px",
-              borderRadius: "6px",
-              border: "1px solid #e5e7eb",
-              color: "#374151"
-            }}>
-              {llmExplanation || 
-                <span style={{ color: "#9ca3af", fontStyle: "italic" }}>
-                  Click "Analyze Code" to get explanation
-                </span>
-              }
-            </div>
-            {llmExplanation && (
-              <div style={{
-                marginTop: "8px",
-                fontSize: "13px",
-                display: "flex",
-                alignItems: "center",
-                gap: "6px"
-              }}>
-                <span style={{ color: "#6b7280" }}>Confidence:</span>
-                <span style={{
-                  color: getConfidenceColor(),
-                  fontWeight: "600"
-                }}>
-                  {confidence}
-                </span>
-              </div>
-            )}
-          </div>
-
-          {/* Control Buttons */}
-          <div style={{
-            display: "flex",
-            gap: "12px",
-            marginBottom: "16px"
-          }}>
-            <button
-              onClick={analyzeCode}
-              disabled={isAnalyzing || !highlightedCode.trim()}
-              style={{
-                padding: "8px 20px",
-                backgroundColor: isAnalyzing ? "#e5e7eb" : "#3b82f6",
-                color: isAnalyzing ? "#9ca3af" : "white",
-                border: "none",
-                borderRadius: "6px",
-                cursor: (isAnalyzing || !highlightedCode.trim()) ? "not-allowed" : "pointer",
-                fontSize: "14px",
-                fontWeight: "500",
-                transition: "background-color 0.2s"
-              }}
-            >
-              {isAnalyzing ? "Analyzing..." : "Analyze Code"}
-            </button>
-          </div>
-
-          {/* Test Execution Section (Optional) */}
-          <details style={{ marginTop: "20px" }}>
-            <summary style={{
-              cursor: "pointer",
-              fontSize: "14px",
-              fontWeight: "600",
-              color: "#4b5563",
-              marginBottom: "12px",
-              userSelect: "none"
-            }}>
-              Test Execution (Optional)
-            </summary>
-            
-            <div style={{
-              backgroundColor: "#f9fafb",
-              padding: "16px",
-              borderRadius: "8px",
-              marginTop: "8px"
-            }}>
-              <div style={{ marginBottom: "12px" }}>
-                <label style={{
-                  display: "block",
-                  marginBottom: "6px",
-                  fontSize: "13px",
-                  fontWeight: "500",
-                  color: "#374151"
-                }}>
-                  Test Inputs:
-                </label>
-                <input
-                  value={testInputs}
-                  onChange={(e) => setTestInputs(e.target.value)}
-                  placeholder="e.g., [3, 5, 2, 8, 1], 0, 4"
-                  style={{
-                    width: "100%",
-                    padding: "8px",
-                    borderRadius: "4px",
-                    border: "1px solid #d1d5db",
-                    fontSize: "13px",
-                    fontFamily: "monospace"
-                  }}
-                />
-              </div>
-
-              <button
-                onClick={executeCode}
-                style={{
-                  padding: "6px 16px",
-                  backgroundColor: "#10b981",
-                  color: "white",
-                  border: "none",
-                  borderRadius: "4px",
-                  cursor: "pointer",
-                  fontSize: "13px",
-                  fontWeight: "500",
-                  marginBottom: "12px"
-                }}
-              >
-                Execute with Test Inputs
-              </button>
-
-              {actualOutput !== null && (
-                <div style={{
-                  backgroundColor: "white",
-                  padding: "10px",
-                  borderRadius: "4px",
-                  border: "1px solid #d1d5db",
-                  marginTop: "8px"
-                }}>
-                  <div style={{ fontSize: "12px", fontWeight: "600", marginBottom: "4px", color: "#059669" }}>
-                    Actual Output:
-                  </div>
-                  <pre style={{
-                    margin: 0,
-                    fontFamily: "monospace",
-                    fontSize: "12px",
-                    whiteSpace: "pre-wrap",
-                    color: "#1f2937"
-                  }}>
-                    {actualOutput}
-                  </pre>
-                </div>
-              )}
-
-              {executionError && (
-                <div style={{
-                  backgroundColor: "#fef2f2",
-                  padding: "10px",
-                  borderRadius: "4px",
-                  border: "1px solid #fecaca",
-                  marginTop: "8px"
-                }}>
-                  <div style={{ fontSize: "12px", fontWeight: "600", marginBottom: "4px", color: "#dc2626" }}>
-                    Execution Error:
-                  </div>
-                  <pre style={{
-                    margin: 0,
-                    fontFamily: "monospace",
-                    fontSize: "11px",
-                    whiteSpace: "pre-wrap",
-                    color: "#991b1b"
-                  }}>
-                    {executionError}
-                  </pre>
-                </div>
-              )}
-            </div>
-          </details>
-
-          {/* Code Reference */}
-          <details style={{ marginTop: "16px" }}>
-            <summary style={{
-              cursor: "pointer",
-              fontSize: "13px",
-              color: "#6b7280",
-              userSelect: "none"
-            }}>
-              View highlighted code
-            </summary>
-            <pre style={{
-              marginTop: "8px",
-              padding: "10px",
-              backgroundColor: "#f3f4f6",
-              borderRadius: "4px",
-              fontSize: "11px",
-              overflow: "auto",
-              fontFamily: "monospace",
-              color: "#374151"
-            }}>
-              {highlightedCode || "(No code selected)"}
-            </pre>
-          </details>
-        </div>
-      );
-    };
-    const FormalSpecification: React.FC<AnnotationEditorProps> = (props) => {
-    const [highlightedSpec, setHighlightedSpec] = useState({ formal: "", simple: "" });
-    const [isGenerating, setIsGenerating] = useState(false);
-    const [error, setError] = useState<string | null>(null);
-    const [expanded, setExpanded] = useState({ highlighted: true });
-
-    const highlightedCode = props.utils.getText() || "";
-
-    // persist specs to metadata
-    useEffect(() => {
-      props.utils.setMetadata({ highlightedSpec });
-    }, [highlightedSpec]);
-
-    const basePrompt = `
-  You are a formal methods assistant that writes CORRECT formal program specifications
-  for JavaScript code using clear mathematical notation.
-
-  Given the input code, produce two synchronized outputs:
-
-  1. "formal" — a formal specification suitable for program verification,
-    including preconditions, postconditions, invariants, and input-output relations,
-    using symbols like ∀, ∃, ⇒, ∧, ∨, =, and set-builder notation when needed.
-
-  2. "simple" — a plain-English presentation of the same specification (non-mathematical).
-
-  Respond with ONLY valid JSON of this form:
-  {
-    "formal": "...",
-    "simple": "..."
-  }
-  `;
-
-    // normalize LLM output
-    const extractTextFromResponse = (resp: any): string => {
-      if (typeof resp === "string") return resp;
-      if (resp && typeof resp === "object") {
-        if (resp.content) return resp.content;
-        if (resp.text) return resp.text;
-        if (Array.isArray(resp.choices) && resp.choices[0]?.message?.content)
-          return resp.choices[0].message.content;
-        if (Array.isArray(resp)) return resp.map((r) => r.content || r.text || "").join("\n");
-        try {
-          return JSON.stringify(resp);
-        } catch {
-          return String(resp);
-        }
-      }
-      return String(resp);
-    };
-
-    // parse JSON safely
-    const tryParseSpecFromText = (text: string) => {
-      const trimmed = text.trim();
-      try {
-        return { parsed: JSON.parse(trimmed) };
-      } catch {
-        const match = trimmed.match(/\{[\s\S]*\}/);
-        if (match) {
-          try {
-            return { parsed: JSON.parse(match[0]) };
-          } catch {
-            return { error: "Found JSON-like text but parsing failed." };
-          }
-        }
-        return { error: "No valid JSON found in response." };
-      }
-    };
-
-    const generateSpec = async () => {
-      const code = highlightedCode.trim();
-      if (!code) {
-        setError("No code selected for specification generation.");
-        return;
-      }
-
-      setIsGenerating(true);
-      setError(null);
-
-      const prompt: ChatMessage[] = [
-        { role: "system", content: basePrompt },
-        {
-          role: "user",
-          content: `Here is the highlighted code section:\n\n${code}\n\nPlease output JSON with keys "formal" and "simple".`,
-        },
-      ];
-
-      try {
-        const resp = await lmApi.chat(prompt, {
+                `,
+          },
+        ];
+        const parsed = await lmApi.chat(prompt, {
           vendor: "copilot",
           family: "gpt-4o",
-          temperature: 0.2,
+          temperature: 0.3,
         });
-        const text = extractTextFromResponse(resp);
-        const { parsed, error: parseErr } = tryParseSpecFromText(text);
-
-        if (parseErr || !parsed?.formal || !parsed?.simple) {
-          setError("Unable to parse LLM response. Please retry.");
-          return;
-        }
-
-        const cleanSpec = {
-          formal: parsed.formal.trim(),
-          simple: parsed.simple.trim(),
-        };
-
-        setHighlightedSpec(cleanSpec);
-      } catch (err: any) {
-        setError(`Error generating specification: ${err.message || String(err)}`);
-      } finally {
-        setIsGenerating(false);
-      }
-    };
-
-    const renderSplitBox = (
-      title: string,
-      spec: { formal: string; simple: string }
-    ) => {
-      const isOpen = expanded.highlighted;
-      return (
-        <details
-          open={isOpen}
-          onToggle={(e) =>
-            setExpanded((prev) => ({
-              ...prev,
-              highlighted: (e.target as HTMLDetailsElement).open,
-            }))
-          }
-          style={{
-            marginBottom: "16px",
-            border: "1px solid #ccc",
-            borderRadius: "6px",
-            backgroundColor: "#fafafa",
-            overflow: "hidden",
-          }}
-        >
-          <summary
-            style={{
-              cursor: "pointer",
-              fontWeight: 600,
-              fontSize: "15px",
-              padding: "10px 12px",
-              backgroundColor: "#f3f4f6",
-              borderBottom: "1px solid #ddd",
-              userSelect: "none",
-            }}
-          >
-            {title}
-          </summary>
-          <div style={{ display: "flex", minHeight: "180px" }}>
-            <div
-              style={{
-                flex: 1,
-                padding: "12px",
-                backgroundColor: "#f9fafb",
-                borderRight: "1px solid #ddd",
-                fontFamily: "monospace",
-                fontSize: "13px",
-                whiteSpace: "pre-wrap",
-              }}
-            >
-              <strong>Formal Specification</strong>
-              <hr />
-              {spec.formal || (
-                <span style={{ color: "#999" }}>No specification yet</span>
-              )}
-            </div>
-            <div
-              style={{
-                flex: 1,
-                padding: "12px",
-                backgroundColor: "#ffffff",
-                fontFamily: "Poppins, sans-serif",
-                fontSize: "13px",
-                lineHeight: "1.5",
-                whiteSpace: "pre-wrap",
-              }}
-            >
-              <strong>Plain-English Explanation</strong>
-              <hr />
-              {spec.simple || (
-                <span style={{ color: "#999" }}>No explanation yet</span>
-              )}
-            </div>
-          </div>
-        </details>
-      );
-    };
-
-    return (
-      <div
-        style={{
-          fontFamily: "Poppins, sans-serif",
-          fontSize: "14px",
-          color: "#333",
-          padding: "12px",
-        }}
-      >
-        <h3 style={{ marginBottom: "12px", fontWeight: "600" }}>
-          🧮 Formal Program Specification Generator
-        </h3>
-
-        <div
-          style={{
-            display: "flex",
-            gap: "10px",
-            marginBottom: "16px",
-            flexWrap: "wrap",
-          }}
-        >
-          <button
-            onClick={() => generateSpec()}
-            disabled={isGenerating}
-            style={{
-              padding: "8px 16px",
-              backgroundColor: "#2563eb",
-              color: "white",
-              border: "none",
-              borderRadius: "4px",
-              cursor: isGenerating ? "not-allowed" : "pointer",
-              fontWeight: "500",
-            }}
-          >
-            {isGenerating ? "Generating..." : "Generate Specification"}
-          </button>
-        </div>
-
-        {error && (
-          <div
-            style={{
-              backgroundColor: "#fef2f2",
-              border: "1px solid #fecaca",
-              color: "#b91c1c",
-              padding: "10px",
-              borderRadius: "4px",
-              marginBottom: "16px",
-              fontSize: "13px",
-            }}
-          >
-            ⚠️ {error}
-          </div>
-        )}
-
-        {renderSplitBox("Specification for Highlighted Code", highlightedSpec)}
-      </div>
-    );
-  };
-  const Generator: React.FC<AnnotationEditorProps> = (props) => {
-  // State management
-  const [userInput, setUserInput] = useState(props.value.metadata.userInput || '');
-  const [generatedCode, setGeneratedCode] = useState(props.value.metadata.generatedCode || '');
-  const [isGenerating, setIsGenerating] = useState(false);
-  const [error, setError] = useState<string | null>(null);
-  const [useMock, setUseMock] = useState(false);
-  const [apiDiagnostics, setApiDiagnostics] = useState<string>('');
-  const [GeneratedComponent, setGeneratedComponent] = useState<React.FC<AnnotationEditorProps> | null>(null);
-  
-  const isMounted = useRef(true);
 
-  // Fallback mock API - only used when real API completely fails
-  // This does NOT generate predetermined templates - it shows the actual error
-  const fallbackMockLmApi = {
-    chat: async (messages: any, options?: any, errorDetails?: string) => {
-      console.log('[FallbackMockAPI] Real API failed - showing error component with details');
-      
-      // Escape the error message for safe inclusion in JavaScript string
-      const safeErrorDetails = (errorDetails || 'Unknown error')
-        .replace(/\\/g, '\\\\')
-        .replace(/'/g, "\\'")
-        .replace(/"/g, '\\"')
-        .replace(/\n/g, '\\n')
-        .replace(/\r/g, '\\r');
-      
-      // Return an error component that displays the actual error
-      return `
-const [showDetails, setShowDetails] = useState(false);
-
-console.log('[FallbackComponent] Real API failed, showing error');
-
-return React.createElement('div',
-  { style: { padding: '10px', fontFamily: 'Poppins, sans-serif' } },
-  React.createElement('div',
-    { style: { padding: '12px', backgroundColor: '#FED9CC', border: '2px solid #D83B01', borderRadius: '6px', marginBottom: '10px' } },
-    React.createElement('h3', 
-      { style: { ...commonTextStyle, marginBottom: '10px', color: '#D83B01', fontSize: '16px' } },
-      '⚠️ API Error'
-    ),
-    React.createElement('p',
-      { style: { ...commonTextStyle, fontSize: '13px', marginBottom: '10px' } },
-      'The component generation API failed. See error details below:'
-    ),
-    React.createElement('div',
-      { style: { marginTop: '10px', marginBottom: '10px' } },
-      React.createElement('button',
-        {
-          onClick: () => setShowDetails(!showDetails),
-          style: {
-            padding: '6px 12px',
-            backgroundColor: '#D83B01',
-            color: 'white',
-            border: 'none',
-            borderRadius: '4px',
-            cursor: 'pointer',
-            fontSize: '12px'
-          }
-        },
-        showDetails ? '▼ Hide Error Details' : '▶ Show Error Details'
-      )
-    ),
-    showDetails && React.createElement('pre',
-      {
-        style: {
-          marginTop: '10px',
-          padding: '10px',
-          backgroundColor: '#fff',
-          border: '1px solid #D83B01',
-          borderRadius: '4px',
-          fontSize: '11px',
-          overflow: 'auto',
-          maxHeight: '200px',
-          fontFamily: 'monospace',
-          whiteSpace: 'pre-wrap',
-          wordBreak: 'break-word'
-        }
-      },
-      '${safeErrorDetails}'
-    )
-  ),
-  React.createElement('div',
-    { style: { padding: '10px', backgroundColor: '#F0F0F0', borderRadius: '4px', fontSize: '12px' } },
-    React.createElement('p',
-      { style: { ...commonTextStyle, fontWeight: 'bold', marginBottom: '8px' } },
-      'Your request:'
-    ),
-    React.createElement('p',
-      { style: { ...commonTextStyle, fontSize: '12px', fontStyle: 'italic', marginBottom: '10px' } },
-      props.value.metadata.userInput || 'No request provided'
-    ),
-    React.createElement('p',
-      { style: { ...commonTextStyle, fontWeight: 'bold', marginBottom: '8px' } },
-      'Highlighted text:'
-    ),
-    React.createElement('pre',
-      { style: { ...commonTextStyle, fontSize: '11px', backgroundColor: '#fff', padding: '8px', borderRadius: '4px', overflow: 'auto', maxHeight: '100px' } },
-      props.utils.getText() || 'No text highlighted'
-    )
-  )
-);
-      `.trim();
-    }
-  };
-
-  useEffect(() => {
-    // Comprehensive API diagnostics
-    const diagnostics = [];
-    
-    diagnostics.push('=== API Diagnostics ===');
-    diagnostics.push(`vscode: ${typeof vscode} ${vscode ? '✓' : '✗'}`);
-    diagnostics.push(`lmApi: ${typeof lmApi} ${lmApi ? '✓' : '✗'}`);
-    
-    if (lmApi) {
-      diagnostics.push(`lmApi.chat: ${typeof lmApi.chat} ${typeof lmApi.chat === 'function' ? '✓' : '✗'}`);
-    }
-    
-    diagnostics.push(`fallbackMockLmApi: ${typeof fallbackMockLmApi} ${fallbackMockLmApi ? '✓' : '✗'}`);
-    
-    const diagText = diagnostics.join('\n');
-    setApiDiagnostics(diagText);
-    console.log(diagText);
-    
-    // Only use mock if the real API is not available
-    const lmApiAvailable = typeof lmApi !== 'undefined' && lmApi !== null && typeof lmApi.chat === 'function';
-    
-    if (!lmApiAvailable) {
-      console.warn('[Generator] Real lmApi not available - fallback mode enabled');
-      setUseMock(true);
-    } else {
-      console.log('[Generator] Real lmApi is available');
-      setUseMock(false);
-    }
-    
-    return () => {
-      isMounted.current = false;
-    };
-  }, []);
-
-  // Load existing generated component on mount
-  useEffect(() => {
-    if (generatedCode && isMounted.current) {
-      try {
-        compileComponent(generatedCode);
-      } catch (err) {
-        console.error("[Generator] Failed to compile existing code:", err);
-      }
-    }
-  }, []);
-
-  // Save state to metadata
-  useEffect(() => {
-    props.utils.setMetadata({
-      userInput,
-      generatedCode,
-    });
-  }, [userInput, generatedCode]);
-
-  // Get document context
-  const anchorText = props.utils.getText();
-  const documentText = props.value.document || '';
-  const startPos = props.value.start;
-  const endPos = props.value.end;
-
-  const createFormattedDocument = () => {
-    if (!documentText) return '';
-    
-    const before = documentText.substring(0, startPos);
-    const highlighted = documentText.substring(startPos, endPos);
-    const after = documentText.substring(endPos);
-    
-    return `${before}<<<HIGHLIGHTED>${highlighted}</HIGHLIGHTED>>>${after}`;
-  };
-
-  const generateAnnotation = async () => {
-    if (!userInput.trim()) {
-      setError('Please describe what you want the annotation to do');
-      return;
-    }
-
-    setIsGenerating(true);
-    setError(null);
-
-    try {
-      const formattedDocument = createFormattedDocument();
-      
-      const prompt: ChatMessage[] = [
-        {
-          role: "system",
-          content: `You are an expert React developer creating annotation components for a code annotation system. 
-
-CONTEXT:
-- You will receive a description of what the annotation should do
-- You have access to the highlighted code/text and surrounding document context
-- The annotation component receives props of type AnnotationEditorProps with these key utilities:
-  * props.utils.getText() - gets the highlighted text
-  * props.utils.setText(newText) - updates the highlighted text
-  * props.utils.setMetadata(obj) - persists data across sessions
-  * props.value.metadata - retrieves persisted data
-  * props.value.document - the full document text for context
-  * props.value.start/end - position of highlighted text
-
-CRITICAL REQUIREMENT - NO JSX:
-You MUST use React.createElement() instead of JSX syntax because the code will be compiled without a JSX transformer.
-DO NOT use angle brackets like <div>, <button>, etc.
-Instead use: React.createElement('div', { style: {...} }, 'content')
-
-REQUIREMENTS:
-1. Generate ONLY the component function body using React.createElement
-2. Do NOT include: imports, export statements, or the component function declaration
-3. Use React hooks (useState, useEffect, useRef) as needed - they're available from React destructuring
-4. Store all state in metadata using props.utils.setMetadata() for persistence
-5. Use the commonTextStyle constant for consistent styling: { fontFamily: "Poppins, sans-serif", fontSize: "14px", color: "black" }
-6. Include comprehensive console.log statements for debugging with format: console.log('[ComponentName] message', data)
-7. Handle errors gracefully with try-catch blocks
-8. The lmApi is available with this EXACT signature:
-   const response = await lmApi.chat(messages, { vendor: 'copilot', family: 'gpt-4o', temperature: 0.32 });
-   IMPORTANT: lmApi.chat() returns a STRING directly, NOT an object. Use it like: const text = await lmApi.chat(messages, options);
-9. Use props.value.document to understand code context for better defaults and behavior
-10. Keep explanations and messages concise and user-friendly
-11. GENERATE EXACTLY WHAT THE USER REQUESTS - do not fall back to predetermined templates
-
-OUTPUT FORMAT:
-Return ONLY valid JavaScript code using React.createElement().
-Start directly with useState/useEffect declarations or the return statement.
-DO NOT wrap code in markdown code blocks.
-
-EXAMPLE OUTPUT STRUCTURE:
-const [value, setValue] = useState(props.value.metadata.value || '');
-console.log('[ComponentName] Initialized with value:', value);
-
-useEffect(() => {
-  props.utils.setMetadata({ value });
-}, [value]);
-
-const handleAction = async () => {
-  console.log('[ComponentName] Action triggered');
-  try {
-    const result = await lmApi.chat([
-      { role: 'system', content: 'You are helpful.' },
-      { role: 'user', content: 'Hello' }
-    ], { vendor: 'copilot', family: 'gpt-4o', temperature: 0.5 });
-    console.log('[ComponentName] Got result:', result);
-  } catch (error) {
-    console.error('[ComponentName] Error:', error);
-  }
-};
-
-return React.createElement('div', 
-  { style: { padding: "10px", fontFamily: "Poppins, sans-serif" } },
-  React.createElement('button', 
-    { onClick: handleAction, style: commonTextStyle },
-    'Click Me'
-  ),
-  React.createElement('p', { style: commonTextStyle }, value)
-);`
-        },
-        {
-          role: "user",
-          content: `Create an annotation component based on this EXACT description:
-${userInput}
-
-Document context (highlighted section marked):
-${formattedDocument || 'No document context available'}
-
-Highlighted text:
-${anchorText || 'No text highlighted'}
-
-IMPORTANT: Generate a component that fulfills the EXACT request above. Do not use predetermined templates or generic components. Create custom functionality that matches what the user specifically asked for.
-
-Generate the component implementation now.`
-        }
-      ];
-
-      console.log('[Generator] Starting generation...');
-      console.log('[Generator] Force fallback mode:', useMock);
-      console.log('[Generator] User request:', userInput);
-      
-      let response: string;
-      let apiUsed = 'unknown';
-      
-      if (useMock) {
-        console.log('[Generator] Using fallback API (manual override - NOT RECOMMENDED)');
-        response = await fallbackMockLmApi.chat(prompt, undefined, 'Manual fallback mode enabled - real API was not attempted');
-        apiUsed = 'fallback-manual';
-      } else {
-        console.log('[Generator] Attempting real lmApi...');
-        console.log('[Generator] lmApi type:', typeof lmApi);
-        console.log('[Generator] lmApi.chat type:', typeof lmApi?.chat);
-        
-        try {
-          const startTime = Date.now();
-          response = await lmApi.chat(prompt, {
-            vendor: 'copilot',
-            family: 'gpt-4o',
-            temperature: 0.3
-          });
-          const elapsed = Date.now() - startTime;
-          console.log(`[Generator] Real API succeeded in ${elapsed}ms`);
-          apiUsed = 'real';
-        } catch (apiError: unknown) {
-          console.error('[Generator] Real API failed:', apiError);
-          console.error('[Generator] Error type:', (apiError as any)?.constructor?.name);
-          console.error('[Generator] Error message:', (apiError instanceof Error) ? apiError.message : String(apiError));
-          console.log('[Generator] Falling back to error component');
-          
-          // Format the error details for display
-          let errorDetails = '';
-          if (apiError instanceof Error) {
-            errorDetails = `Error: ${apiError.message}\n\nStack trace:\n${apiError.stack || 'No stack trace available'}`;
-          } else {
-            errorDetails = `Error: ${String(apiError)}\n\nType: ${(apiError as any)?.constructor?.name || 'unknown'}`;
-          }
-          
-          // Add any additional error properties
-          if (typeof apiError === 'object' && apiError !== null) {
-            const errorObj = apiError as any;
-            const extraProps = Object.keys(errorObj).filter(k => k !== 'message' && k !== 'stack' && k !== 'name');
-            if (extraProps.length > 0) {
-              errorDetails += '\n\nAdditional details:\n';
-              extraProps.forEach(prop => {
-                errorDetails += `${prop}: ${JSON.stringify(errorObj[prop], null, 2)}\n`;
-              });
-            }
-          }
-          
-          response = await fallbackMockLmApi.chat(prompt, undefined, errorDetails);
-          apiUsed = 'fallback-auto';
-        }
-      }
-
-      console.log('[Generator] API used:', apiUsed);
-      console.log('[Generator] Response length:', response?.length);
-      console.log('[Generator] Response preview:', response?.substring(0, 100));
-
-      // Extract code from response (remove markdown code blocks if present)
-      let code = response.trim();
-      const codeBlockMatch = code.match(/```(?:javascript|typescript|jsx|tsx)?\n([\s\S]*?)\n```/);
-      if (codeBlockMatch) {
-        code = codeBlockMatch[1].trim();
-        console.log('[Generator] Extracted code from markdown block');
-      }
-
-      console.log('[Generator] Final code length:', code.length);
-      
-      if (isMounted.current) {
-        setGeneratedCode(code);
-        compileComponent(code);
-        console.log('[Generator] Component compiled successfully');
-      }
-    } catch (err) {
-      const errorMsg = err instanceof Error ? err.message : 'An error occurred while generating the annotation';
-      console.error('[Generator] Error:', errorMsg, err);
-      if (isMounted.current) {
-        setError(errorMsg);
-      }
-    } finally {
-      if (isMounted.current) {
-        setIsGenerating(false);
-      }
-    }
-  };
-
-  const compileComponent = (code: string) => {
-    try {
-      console.log('[Generator] Compiling component...');
-      
-      const commonTextStyle = {
-        fontFamily: "Poppins, sans-serif",
-        fontSize: "14px",
-        color: "black",
-      };
-
-      // Create a function that returns a React component
-      const componentFunction = new Function(
-        'React',
-        'props',
-        'lmApi',
-        'mockLmApi',
-        'vscode',
-        'commonTextStyle',
-        `
-        const { useState, useEffect, useRef } = React;
-        ${code}
-        `
-      );
-
-      // Create a wrapper component
-      const WrappedComponent: React.FC<AnnotationEditorProps> = (componentProps) => {
-        return componentFunction(
-          React,
-          componentProps,
-          lmApi,
-          mockLmApi,
-          vscode,
-          commonTextStyle
-        );
+        const newExpression = parsed;
+        setExpression(newExpression);
+        // Store in metadata for persistence
+        props.utils.setMetadata({ expression: newExpression });
+        setRetryParse(false);
       };
 
-      setGeneratedComponent(() => WrappedComponent);
-      console.log('[Generator] Component compiled and set successfully');
-    } catch (err) {
-      console.error('[Generator] Compilation error:', err);
-      throw new Error(`Failed to compile generated component: ${err instanceof Error ? err.message : String(err)}`);
+      parseText(props.utils.getText());
     }
-  };
+  }, [props.utils, retryParse]);
 
-  const resetGenerator = () => {
-    console.log('[Generator] Resetting generator');
-    setGeneratedCode('');
-    setGeneratedComponent(null);
-    setError(null);
+  // Update metadata when user manually edits the expression
+  const handleExpressionChange = (evt: React.ChangeEvent<HTMLInputElement>) => {
+    const newExpression = evt.target.value;
+    setExpression(newExpression);
+    props.utils.setMetadata({ expression: newExpression });
   };
 
-  // If we have a generated component, render it
-  if (GeneratedComponent) {
-    return (
-      <div style={{ padding: "10px", fontFamily: "Poppins, sans-serif" }}>
-        <div style={{
-          marginBottom: "10px",
-          padding: "8px",
-          backgroundColor: "#E8F5E9",
-          border: "1px solid #4CAF50",
-          borderRadius: "4px",
-          fontSize: "12px",
-          display: "flex",
-          justifyContent: "space-between",
-          alignItems: "center"
-        }}>
-          <span>✓ Generated annotation active</span>
-          <button
-            onClick={resetGenerator}
-            style={{
-              padding: "4px 8px",
-              backgroundColor: "#f44336",
-              color: "white",
-              border: "none",
-              borderRadius: "4px",
-              cursor: "pointer",
-              fontSize: "12px"
-            }}
-          >
-            Reset
-          </button>
-        </div>
-        <GeneratedComponent {...props} />
-      </div>
-    );
-  }
+  const odysseyBase = "https://herbie-fp.github.io/odyssey/?spec=";
+  const url = odysseyBase + encodeURIComponent(expression);
 
-  // Otherwise, show the input interface
   return (
-    <div style={{ padding: "10px", fontFamily: "Poppins, sans-serif" }}>
-      {apiDiagnostics && (
-        <details style={{ marginBottom: "15px", fontSize: "11px", color: "#666" }}>
-          <summary style={{ cursor: "pointer", fontWeight: "bold" }}>
-            API Diagnostics (click to expand)
-          </summary>
-          <pre style={{
-            marginTop: "8px",
-            padding: "8px",
-            backgroundColor: "#f5f5f5",
-            borderRadius: "4px",
-            overflow: "auto"
-          }}>
-            {apiDiagnostics}
-          </pre>
-        </details>
-      )}
-      
-      <div style={{ marginBottom: "12px" }}>
-        <label style={{
-          display: "block",
-          marginBottom: "6px",
-          fontWeight: "bold",
-          fontSize: "14px"
-        }}>
-          Describe the annotation you want to create:
-        </label>
-        <textarea
-          value={userInput}
-          onChange={(e) => setUserInput(e.target.value)}
-          placeholder="Example: Create a color picker that lets me change the hex color value in this code... or Create a timer that counts down from the number in this variable..."
-          style={{
-            width: "100%",
-            padding: "8px",
-            borderRadius: "4px",
-            border: "1px solid #ccc",
-            fontSize: "14px",
-            minHeight: "80px",
-            resize: "vertical",
-            fontFamily: "Poppins, sans-serif"
-          }}
-        />
-      </div>
-
-      <div style={{ marginBottom: "15px", display: "flex", gap: "10px", alignItems: "center" }}>
+    <div className="odyssey">
+      <p>Parsed the following original expression from highlighted text:</p>
+      <input
+        type="text"
+        className="odyssey-text"
+        onChange={handleExpressionChange}
+        value={expression}
+      />
+      <button onClick={() => setRetryParse(true)}>Retry</button>
+      <p>
+        Explore floating-point error in this expression with
         <button
-          onClick={generateAnnotation}
-          disabled={isGenerating || !userInput.trim()}
-          style={{
-            padding: "6px 12px",
-            backgroundColor: isGenerating ? "#cccccc" : "#0078D4",
-            color: "white",
-            border: "none",
-            borderRadius: "4px",
-            cursor: isGenerating ? "default" : "pointer",
-            fontSize: "14px"
-          }}
-        >
-          {isGenerating ? "Generating..." : "Generate"}
+          className="open-external"
+          onClick={() => vscode.postMessage({ command: "open-external", url })}>
+          Odyssey
+          <svg
+            className="open-external-icon"
+            xmlns="http://www.w3.org/2000/svg"
+            viewBox="0 0 256 256">
+            <path d="M224,104a8,8,0,0,1-16,0V59.32l-66.33,66.34a8,8,0,0,1-11.32-11.32L196.68,48H152a8,8,0,0,1,0-16h64a8,8,0,0,1,8,8Zm-40,24a8,8,0,0,0-8,8v72H48V80h72a8,8,0,0,0,0-16H48A16,16,0,0,0,32,80V208a16,16,0,0,0,16,16H176a16,16,0,0,0,16-16V136A8,8,0,0,0,184,128Z"></path>
+          </svg>
         </button>
-
-        <label style={{
-          display: "flex",
-          alignItems: "center",
-          fontSize: "12px",
-          cursor: "pointer",
-          marginLeft: "10px"
-        }}>
-          <input
-            type="checkbox"
-            checked={useMock}
-            onChange={() => setUseMock(!useMock)}
-            style={{ marginRight: "5px" }}
-          />
-          Force fallback mode (shows error - for testing only)
-        </label>
-        
-        <span style={{ fontSize: "11px", color: "#666", marginLeft: "10px" }}>
-          {useMock ? "⚠️ Fallback Mode" : "✓ Real API"}
-        </span>
-      </div>
-
-      {error && (
-        <div style={{
-          color: "#D83B01",
-          backgroundColor: "#FED9CC",
-          padding: "8px",
-          borderRadius: "4px",
-          marginBottom: "12px",
-          fontSize: "14px"
-        }}>
-          {error}
-        </div>
-      )}
-
-      {generatedCode && !GeneratedComponent && (
-        <div style={{
-          marginTop: "15px",
-          padding: "10px",
-          backgroundColor: "#FFF3CD",
-          border: "1px solid #FFC107",
-          borderRadius: "4px",
-          fontSize: "12px"
-        }}>
-          <strong>Generated code (failed to compile):</strong>
-          <pre style={{
-            marginTop: "8px",
-            padding: "8px",
-            backgroundColor: "#F5F5F5",
-            borderRadius: "4px",
-            overflow: "auto",
-            maxHeight: "200px",
-            fontSize: "11px"
-          }}>
-            {generatedCode}
-          </pre>
-        </div>
-      )}
-
-      <div style={{
-        marginTop: "15px",
-        padding: "10px",
-        backgroundColor: "#F0F0F0",
-        borderRadius: "4px",
-        fontSize: "12px",
-        color: "#666"
-      }}>
-        <strong>Tips:</strong>
-        <ul style={{ marginTop: "5px", marginBottom: "0", paddingLeft: "20px" }}>
-          <li>Be specific about what the annotation should do</li>
-          <li>Describe the exact behavior and UI you want</li>
-          <li>Mention if it should interact with the highlighted text</li>
-          <li>State if data should persist across sessions</li>
-          <li>Examples: "rating stars", "color picker", "countdown timer", "progress tracker"</li>
-        </ul>
-      </div>
+      </p>
     </div>
   );
 };
 
+/* TODO: Add all tools to be used here. */
+export const tools = {
+  comment: Comment,
+  colorPicker: ColorPicker,
+  // runCodeSegment: RunCodeSegment,
+  imageUpload: ImageUpload,
+  displayHTML: DisplayHTML,
+  odyssey: Odyssey,
+  yesNoQuestion: LMUnitTest,
+  debugExample: ShowDebuggedExample,
+  explainInEnglish: ExplainInEnglish,
+  outputVisualizer: OutputVisualizer,
+  formalSpecification: FormalSpecification,
+  Generator: Generator,
+  // lmApiTest: LMAPITest,
+};
 
-
-    /* TODO: Add all tools to be used here. */
-    export const tools = {
-      comment: Comment,
-      colorPicker: ColorPicker,
-      // runCodeSegment: RunCodeSegment,
-      imageUpload: ImageUpload,
-      displayHTML: DisplayHTML,
-      odyssey: Odyssey,
-      yesNoQuestion: LMUnitTest,
-      debugExample: ShowDebuggedExample,
-      explainInEnglish: ExplainInEnglish, 
-      outputVisualizer: OutputVisualizer,
-      formalSpecification: FormalSpecification, 
-      Generator: Generator,
-      // lmApiTest: LMAPITest,
-    };
-
-    export const toolNames = {
-      comment: "Comment",
-      colorPicker: "Color Picker",
-      // runCodeSegment: "Run Code Segment",
-      imageUpload: "Image Upload",
-      displayHTML: "HTML Preview",
-      odyssey: "Analyze Floating-point Expression",
-      yesNoQuestion: "LM Unit Test",
-      debugExample: "Show Debugged Example",
-      explainInEnglish: "Explain in English",
-      outputVisualizer: "Output Visualizer",
-      formalSpecification: "Formal Specification",
-      Generator: "Annotation Generator",
-      // lmApiTest: "LM API Test",
-    };
+export const toolNames = {
+  comment: "Comment",
+  colorPicker: "Color Picker",
+  // runCodeSegment: "Run Code Segment",
+  imageUpload: "Image Upload",
+  displayHTML: "HTML Preview",
+  odyssey: "Analyze Floating-point Expression",
+  yesNoQuestion: "LM Unit Test",
+  debugExample: "Show Debugged Example",
+  explainInEnglish: "Explain in English",
+  outputVisualizer: "Output Visualizer",
+  formalSpecification: "Formal Specification",
+  Generator: "Annotation Generator",
+  // lmApiTest: "LM API Test",
+};

From a3655e0f6cf2ea303063da79cdc8c80940c86ce1 Mon Sep 17 00:00:00 2001
From: Edward Misback <misback@cs.washington.edu>
Date: Wed, 25 Mar 2026 05:26:53 -0400
Subject: [PATCH 02/22] Add session link to Odyssey component.

---
 vscode-extension/webview-ui/src/tools.tsx | 37 +++++++++++++++++++++--
 1 file changed, 35 insertions(+), 2 deletions(-)

diff --git a/vscode-extension/webview-ui/src/tools.tsx b/vscode-extension/webview-ui/src/tools.tsx
index d1e8698..febe5f8 100644
--- a/vscode-extension/webview-ui/src/tools.tsx
+++ b/vscode-extension/webview-ui/src/tools.tsx
@@ -225,6 +225,7 @@ const DisplayHTML: React.FC<AnnotationEditorProps> = (props) => {
 const Odyssey: React.FC<AnnotationEditorProps> = (props) => {
   const [expression, setExpression] = useState(props.value.metadata.expression || "loading...");
   const [retryParse, setRetryParse] = useState(false);
+  const [sessionLink, setSessionLink] = useState(props.value.metadata.odysseySessionLink || "");
 
   useEffect(() => {
     // Only make API call if expression is "loading..." or retry was clicked
@@ -255,7 +256,6 @@ const Odyssey: React.FC<AnnotationEditorProps> = (props) => {
 
         const newExpression = parsed;
         setExpression(newExpression);
-        // Store in metadata for persistence
         props.utils.setMetadata({ expression: newExpression });
         setRetryParse(false);
       };
@@ -264,13 +264,34 @@ const Odyssey: React.FC<AnnotationEditorProps> = (props) => {
     }
   }, [props.utils, retryParse]);
 
-  // Update metadata when user manually edits the expression
   const handleExpressionChange = (evt: React.ChangeEvent<HTMLInputElement>) => {
     const newExpression = evt.target.value;
     setExpression(newExpression);
     props.utils.setMetadata({ expression: newExpression });
   };
 
+  const handleSessionLinkChange = (evt: React.ChangeEvent<HTMLInputElement>) => {
+    const newLink = evt.target.value;
+    setSessionLink(newLink);
+    props.utils.setMetadata({ odysseySessionLink: newLink });
+  };
+
+  const openSessionLink = () => {
+    const urlToOpen = sessionLink.trim();
+    if (!urlToOpen) return;
+    vscode.postMessage({ command: "open-external", url: urlToOpen });
+  };
+
+  const isValidSessionLink = (() => {
+    try {
+      if (!sessionLink.trim()) return false;
+      new URL(sessionLink.trim());
+      return true;
+    } catch {
+      return false;
+    }
+  })();
+
   const odysseyBase = "https://herbie-fp.github.io/odyssey/?spec=";
   const url = odysseyBase + encodeURIComponent(expression);
 
@@ -298,6 +319,18 @@ const Odyssey: React.FC<AnnotationEditorProps> = (props) => {
           </svg>
         </button>
       </p>
+
+      <p>Paste and save your Odyssey session link:</p>
+      <input
+        type="url"
+        className="odyssey-text"
+        placeholder="https://herbie-fp.github.io/odyssey/..."
+        value={sessionLink}
+        onChange={handleSessionLinkChange}
+      />
+      <button onClick={openSessionLink} disabled={!isValidSessionLink}>
+        Open saved session
+      </button>
     </div>
   );
 };

From b17f41b7c4c08a9fcb9cdb23e3c4c7db37022bfa Mon Sep 17 00:00:00 2001
From: Edward Misback <misback@cs.washington.edu>
Date: Thu, 26 Mar 2026 13:55:35 -0400
Subject: [PATCH 03/22] Add MarkdownEditor

---
 .../webview-ui/src/MarkdownEditor.tsx         | 319 ++++++++++++++++++
 vscode-extension/webview-ui/src/tools.tsx     |   4 +
 2 files changed, 323 insertions(+)
 create mode 100644 vscode-extension/webview-ui/src/MarkdownEditor.tsx

diff --git a/vscode-extension/webview-ui/src/MarkdownEditor.tsx b/vscode-extension/webview-ui/src/MarkdownEditor.tsx
new file mode 100644
index 0000000..15268f2
--- /dev/null
+++ b/vscode-extension/webview-ui/src/MarkdownEditor.tsx
@@ -0,0 +1,319 @@
+// ─── MarkdownEditor (true WYSIWYG) ──────────────────────────────────
+//
+// Install:
+//   npm install @tiptap/react @tiptap/starter-kit @tiptap/extension-image \
+//               @tiptap/extension-placeholder
+//
+// In tools.tsx, add these imports at the top:
+//
+//   import { useEditor, EditorContent } from "@tiptap/react";
+//   import StarterKit from "@tiptap/starter-kit";
+//   import Image from "@tiptap/extension-image";
+//   import Placeholder from "@tiptap/extension-placeholder";
+//
+// Then paste the component (everything below) before `export const tools`.
+// The tools/toolNames exports already reference MarkdownEditor, so no
+// further changes are needed.
+// ─────────────────────────────────────────────────────────────────────
+
+import { useEditor, EditorContent } from "@tiptap/react";
+import StarterKit from "@tiptap/starter-kit";
+import Image from "@tiptap/extension-image";
+import Placeholder from "@tiptap/extension-placeholder";
+import { AnnotationEditorProps } from "./App";
+import React, { useRef } from "react";
+
+
+
+
+/* ── helper ─────────────────────────────────────────────────────────── */
+
+function readFileAsDataURL(file: File | Blob): Promise<string> {
+  return new Promise((resolve, reject) => {
+    const reader = new FileReader();
+    reader.onload = () => resolve(reader.result as string);
+    reader.onerror = () => reject(reader.error);
+    reader.readAsDataURL(file);
+  });
+}
+
+/* ── toolbar button ─────────────────────────────────────────────────── */
+
+const TBButton: React.FC<{
+  onClick: () => void;
+  active?: boolean;
+  title?: string;
+  children: React.ReactNode;
+}> = ({ onClick, active, title, children }) => (
+  <button
+    type="button"
+    title={title}
+    onMouseDown={(e) => {
+      e.preventDefault(); // keep editor focus
+      onClick();
+    }}
+    style={{
+      padding: "2px 6px",
+      fontSize: 13,
+      fontFamily: "Poppins, sans-serif",
+      border: "1px solid #ccc",
+      borderRadius: 3,
+      background: active ? "#e0e0e0" : "#fafafa",
+      cursor: "pointer",
+      lineHeight: 1.4,
+    }}
+  >
+    {children}
+  </button>
+);
+
+/* ── component ──────────────────────────────────────────────────────── */
+
+const MarkdownNote: React.FC<AnnotationEditorProps> = (props) => {
+  const fileInputRef = useRef<HTMLInputElement>(null);
+
+  const editor = useEditor({
+    extensions: [
+      StarterKit,
+      Image.configure({ inline: true, allowBase64: true }),
+      Placeholder.configure({ placeholder: "Write your note here…" }),
+    ],
+    content: props.value.metadata.markdownContent ?? "",
+    onUpdate: ({ editor }) => {
+      props.utils.setMetadata({ markdownContent: editor.getHTML() });
+    },
+    editorProps: {
+      // ── paste images from clipboard ──
+      handlePaste: (view, event) => {
+        const items = event.clipboardData?.items;
+        if (!items) return false;
+
+        for (const item of Array.from(items)) {
+          if (item.type.startsWith("image/")) {
+            event.preventDefault();
+            const blob = item.getAsFile();
+            if (blob) {
+              readFileAsDataURL(blob).then((src) => {
+                view.dispatch(
+                  view.state.tr.replaceSelectionWith(
+                    view.state.schema.nodes.image.create({ src })
+                  )
+                );
+              });
+            }
+            return true;
+          }
+        }
+        return false;
+      },
+      // ── drop images from desktop / file manager ──
+      handleDrop: (view, event) => {
+        const files = event.dataTransfer?.files;
+        if (!files || files.length === 0) return false;
+
+        const file = files[0];
+        if (!file.type.startsWith("image/")) return false;
+
+        event.preventDefault();
+        const coords = view.posAtCoords({
+          left: event.clientX,
+          top: event.clientY,
+        });
+
+        readFileAsDataURL(file).then((src) => {
+          const node = view.state.schema.nodes.image.create({ src });
+          if (coords) {
+            view.dispatch(view.state.tr.insert(coords.pos, node));
+          } else {
+            view.dispatch(view.state.tr.replaceSelectionWith(node));
+          }
+        });
+
+        return true;
+      },
+    },
+  });
+
+  const insertImageFromFile = React.useCallback(
+    async (e: React.ChangeEvent<HTMLInputElement>) => {
+      const file = e.target.files?.[0];
+      if (!file || !editor) return;
+      const src = await readFileAsDataURL(file);
+      editor.chain().focus().setImage({ src }).run();
+      e.target.value = "";
+    },
+    [editor]
+  );
+
+  if (!editor) return null;
+
+  return (
+    <div style={{ fontFamily: "Poppins, sans-serif" }}>
+      {/* ── toolbar ── */}
+      <div
+        style={{
+          display: "flex",
+          flexWrap: "wrap",
+          gap: 3,
+          padding: "4px 0 6px",
+          borderBottom: "1px solid #ddd",
+          marginBottom: 6,
+        }}
+      >
+        <TBButton
+          onClick={() => editor.chain().focus().toggleBold().run()}
+          active={editor.isActive("bold")}
+          title="Bold"
+        >
+          <b>B</b>
+        </TBButton>
+        <TBButton
+          onClick={() => editor.chain().focus().toggleItalic().run()}
+          active={editor.isActive("italic")}
+          title="Italic"
+        >
+          <i>I</i>
+        </TBButton>
+        <TBButton
+          onClick={() => editor.chain().focus().toggleStrike().run()}
+          active={editor.isActive("strike")}
+          title="Strikethrough"
+        >
+          <s>S</s>
+        </TBButton>
+        <TBButton
+          onClick={() => editor.chain().focus().toggleCode().run()}
+          active={editor.isActive("code")}
+          title="Inline code"
+        >
+          {"</>"}
+        </TBButton>
+
+        <span style={{ borderLeft: "1px solid #ccc", margin: "0 2px" }} />
+
+        <TBButton
+          onClick={() => editor.chain().focus().toggleHeading({ level: 2 }).run()}
+          active={editor.isActive("heading", { level: 2 })}
+          title="Heading"
+        >
+          H
+        </TBButton>
+        <TBButton
+          onClick={() => editor.chain().focus().toggleBulletList().run()}
+          active={editor.isActive("bulletList")}
+          title="Bullet list"
+        >
+          •&thinsp;list
+        </TBButton>
+        <TBButton
+          onClick={() => editor.chain().focus().toggleOrderedList().run()}
+          active={editor.isActive("orderedList")}
+          title="Ordered list"
+        >
+          1.&thinsp;list
+        </TBButton>
+        <TBButton
+          onClick={() => editor.chain().focus().toggleBlockquote().run()}
+          active={editor.isActive("blockquote")}
+          title="Blockquote"
+        >
+          &ldquo;&thinsp;&rdquo;
+        </TBButton>
+        <TBButton
+          onClick={() => editor.chain().focus().toggleCodeBlock().run()}
+          active={editor.isActive("codeBlock")}
+          title="Code block"
+        >
+          {"{ }"}
+        </TBButton>
+
+        <span style={{ borderLeft: "1px solid #ccc", margin: "0 2px" }} />
+
+        <TBButton onClick={() => fileInputRef.current?.click()} title="Upload image">
+          <span style={{ display: "inline-flex", alignItems: "center", gap: 3 }}>
+            <svg
+              xmlns="http://www.w3.org/2000/svg"
+              width="13"
+              height="13"
+              viewBox="0 0 24 24"
+              fill="none"
+              stroke="currentColor"
+              strokeWidth="2"
+              strokeLinecap="round"
+              strokeLinejoin="round"
+            >
+              <rect x="3" y="3" width="18" height="18" rx="2" ry="2" />
+              <circle cx="8.5" cy="8.5" r="1.5" />
+              <polyline points="21 15 16 10 5 21" />
+            </svg>
+            Image
+          </span>
+        </TBButton>
+      </div>
+
+      {/* ── editor surface ── */}
+      <EditorContent
+        editor={editor}
+        style={{
+          minHeight: 180,
+          maxHeight: 400,
+          overflowY: "auto",
+          border: "1px solid #ccc",
+          borderRadius: 4,
+          padding: 8,
+          fontSize: 13,
+          lineHeight: 1.5,
+        }}
+      />
+
+      {/* hidden file input for the Image toolbar button */}
+      <input
+        ref={fileInputRef}
+        type="file"
+        accept="image/*"
+        onChange={insertImageFromFile}
+        style={{ display: "none" }}
+      />
+
+      {/* ── inline styles for the Tiptap content area ── */}
+      <style>{`
+        .tiptap {
+          outline: none;
+        }
+        .tiptap p.is-editor-empty:first-child::before {
+          content: attr(data-placeholder);
+          float: left;
+          color: #aaa;
+          pointer-events: none;
+          height: 0;
+        }
+        .tiptap img {
+          max-width: 100%;
+          height: auto;
+          border-radius: 4px;
+          margin: 6px 0;
+        }
+        .tiptap pre {
+          background: #f4f4f4;
+          padding: 8px 12px;
+          border-radius: 4px;
+          overflow-x: auto;
+        }
+        .tiptap blockquote {
+          border-left: 3px solid #ccc;
+          padding-left: 10px;
+          margin-left: 0;
+          color: #555;
+        }
+        .tiptap code {
+          background: #f0f0f0;
+          padding: 1px 4px;
+          border-radius: 3px;
+          font-size: 0.9em;
+        }
+      `}</style>
+    </div>
+  );
+};
+
+export default MarkdownNote;
\ No newline at end of file
diff --git a/vscode-extension/webview-ui/src/tools.tsx b/vscode-extension/webview-ui/src/tools.tsx
index febe5f8..fd43e46 100644
--- a/vscode-extension/webview-ui/src/tools.tsx
+++ b/vscode-extension/webview-ui/src/tools.tsx
@@ -14,6 +14,8 @@ import {
   OutputVisualizer,
 } from "./additionalTools";
 
+import MarkdownNote from "./MarkdownEditor";
+
 type AnnotationType = React.FC<AnnotationEditorProps>;
 interface ImageData {
   file: File;
@@ -349,6 +351,7 @@ export const tools = {
   outputVisualizer: OutputVisualizer,
   formalSpecification: FormalSpecification,
   Generator: Generator,
+  MarkdownNote: MarkdownNote,
   // lmApiTest: LMAPITest,
 };
 
@@ -365,5 +368,6 @@ export const toolNames = {
   outputVisualizer: "Output Visualizer",
   formalSpecification: "Formal Specification",
   Generator: "Annotation Generator",
+  MarkdownNote: "Markdown Note",
   // lmApiTest: "LM API Test",
 };

From 817f2aba7264642b8c3d04e5daf0dddd57e58592 Mon Sep 17 00:00:00 2001
From: Edward Misback <misback@cs.washington.edu>
Date: Fri, 27 Mar 2026 01:37:11 -0400
Subject: [PATCH 04/22] Implement resizable md editor

---
 .../webview-ui/src/MarkdownEditor.tsx         | 114 +++++++++++++-----
 1 file changed, 87 insertions(+), 27 deletions(-)

diff --git a/vscode-extension/webview-ui/src/MarkdownEditor.tsx b/vscode-extension/webview-ui/src/MarkdownEditor.tsx
index 15268f2..c04e89a 100644
--- a/vscode-extension/webview-ui/src/MarkdownEditor.tsx
+++ b/vscode-extension/webview-ui/src/MarkdownEditor.tsx
@@ -27,7 +27,7 @@ import React, { useRef } from "react";
 
 
 /* ── helper ─────────────────────────────────────────────────────────── */
-
+ 
 function readFileAsDataURL(file: File | Blob): Promise<string> {
   return new Promise((resolve, reject) => {
     const reader = new FileReader();
@@ -36,9 +36,9 @@ function readFileAsDataURL(file: File | Blob): Promise<string> {
     reader.readAsDataURL(file);
   });
 }
-
+ 
 /* ── toolbar button ─────────────────────────────────────────────────── */
-
+ 
 const TBButton: React.FC<{
   onClick: () => void;
   active?: boolean;
@@ -66,12 +66,20 @@ const TBButton: React.FC<{
     {children}
   </button>
 );
-
+ 
 /* ── component ──────────────────────────────────────────────────────── */
-
+ 
+const DEFAULT_EDITOR_HEIGHT = 180;
+const MIN_EDITOR_HEIGHT = 80;
+ 
 const MarkdownNote: React.FC<AnnotationEditorProps> = (props) => {
   const fileInputRef = useRef<HTMLInputElement>(null);
-
+  const editorWrapperRef = useRef<HTMLDivElement>(null);
+  const dragState = useRef<{ startY: number; startH: number } | null>(null);
+ 
+  const editorHeight: number =
+    props.value.metadata.editorHeight ?? DEFAULT_EDITOR_HEIGHT;
+ 
   const editor = useEditor({
     extensions: [
       StarterKit,
@@ -87,7 +95,7 @@ const MarkdownNote: React.FC<AnnotationEditorProps> = (props) => {
       handlePaste: (view, event) => {
         const items = event.clipboardData?.items;
         if (!items) return false;
-
+ 
         for (const item of Array.from(items)) {
           if (item.type.startsWith("image/")) {
             event.preventDefault();
@@ -110,16 +118,16 @@ const MarkdownNote: React.FC<AnnotationEditorProps> = (props) => {
       handleDrop: (view, event) => {
         const files = event.dataTransfer?.files;
         if (!files || files.length === 0) return false;
-
+ 
         const file = files[0];
         if (!file.type.startsWith("image/")) return false;
-
+ 
         event.preventDefault();
         const coords = view.posAtCoords({
           left: event.clientX,
           top: event.clientY,
         });
-
+ 
         readFileAsDataURL(file).then((src) => {
           const node = view.state.schema.nodes.image.create({ src });
           if (coords) {
@@ -128,12 +136,12 @@ const MarkdownNote: React.FC<AnnotationEditorProps> = (props) => {
             view.dispatch(view.state.tr.replaceSelectionWith(node));
           }
         });
-
+ 
         return true;
       },
     },
   });
-
+ 
   const insertImageFromFile = React.useCallback(
     async (e: React.ChangeEvent<HTMLInputElement>) => {
       const file = e.target.files?.[0];
@@ -144,9 +152,9 @@ const MarkdownNote: React.FC<AnnotationEditorProps> = (props) => {
     },
     [editor]
   );
-
+ 
   if (!editor) return null;
-
+ 
   return (
     <div style={{ fontFamily: "Poppins, sans-serif" }}>
       {/* ── toolbar ── */}
@@ -188,9 +196,9 @@ const MarkdownNote: React.FC<AnnotationEditorProps> = (props) => {
         >
           {"</>"}
         </TBButton>
-
+ 
         <span style={{ borderLeft: "1px solid #ccc", margin: "0 2px" }} />
-
+ 
         <TBButton
           onClick={() => editor.chain().focus().toggleHeading({ level: 2 }).run()}
           active={editor.isActive("heading", { level: 2 })}
@@ -226,9 +234,9 @@ const MarkdownNote: React.FC<AnnotationEditorProps> = (props) => {
         >
           {"{ }"}
         </TBButton>
-
+ 
         <span style={{ borderLeft: "1px solid #ccc", margin: "0 2px" }} />
-
+ 
         <TBButton onClick={() => fileInputRef.current?.click()} title="Upload image">
           <span style={{ display: "inline-flex", alignItems: "center", gap: 3 }}>
             <svg
@@ -250,22 +258,74 @@ const MarkdownNote: React.FC<AnnotationEditorProps> = (props) => {
           </span>
         </TBButton>
       </div>
-
+ 
       {/* ── editor surface ── */}
-      <EditorContent
-        editor={editor}
+      <div
+        ref={editorWrapperRef}
         style={{
-          minHeight: 180,
-          maxHeight: 400,
+          height: editorHeight,
           overflowY: "auto",
           border: "1px solid #ccc",
-          borderRadius: 4,
+          borderRadius: "4px 4px 0 0",
           padding: 8,
           fontSize: 13,
           lineHeight: 1.5,
         }}
-      />
-
+      >
+        <EditorContent editor={editor} />
+      </div>
+ 
+      {/* ── resize handle ── */}
+      <div
+        onPointerDown={(e) => {
+          e.preventDefault();
+          dragState.current = { startY: e.clientY, startH: editorHeight };
+          const onMove = (ev: PointerEvent) => {
+            if (!dragState.current) return;
+            const newH = Math.max(
+              MIN_EDITOR_HEIGHT,
+              dragState.current.startH + (ev.clientY - dragState.current.startY)
+            );
+            // Update the wrapper height directly for responsive feel
+            if (editorWrapperRef.current) {
+              editorWrapperRef.current.style.height = `${newH}px`;
+            }
+          };
+          const onUp = (ev: PointerEvent) => {
+            if (dragState.current) {
+              const finalH = Math.max(
+                MIN_EDITOR_HEIGHT,
+                dragState.current.startH + (ev.clientY - dragState.current.startY)
+              );
+              props.utils.setMetadata({ editorHeight: finalH });
+            }
+            dragState.current = null;
+            document.removeEventListener("pointermove", onMove);
+            document.removeEventListener("pointerup", onUp);
+          };
+          document.addEventListener("pointermove", onMove);
+          document.addEventListener("pointerup", onUp);
+        }}
+        style={{
+          height: 7,
+          cursor: "ns-resize",
+          background: "#eee",
+          borderRadius: "0 0 4px 4px",
+          border: "1px solid #ccc",
+          borderTop: "none",
+          display: "flex",
+          alignItems: "center",
+          justifyContent: "center",
+        }}
+      >
+        {/* grip dots */}
+        <svg width="20" height="4" viewBox="0 0 20 4" fill="#999">
+          <circle cx="4" cy="2" r="1.2" />
+          <circle cx="10" cy="2" r="1.2" />
+          <circle cx="16" cy="2" r="1.2" />
+        </svg>
+      </div>
+ 
       {/* hidden file input for the Image toolbar button */}
       <input
         ref={fileInputRef}
@@ -274,7 +334,7 @@ const MarkdownNote: React.FC<AnnotationEditorProps> = (props) => {
         onChange={insertImageFromFile}
         style={{ display: "none" }}
       />
-
+ 
       {/* ── inline styles for the Tiptap content area ── */}
       <style>{`
         .tiptap {

From af3441b41afe300fb0de7505a40fd25e48de3bd0 Mon Sep 17 00:00:00 2001
From: Edward Misback <misback@cs.washington.edu>
Date: Tue, 7 Apr 2026 00:58:21 -0400
Subject: [PATCH 05/22] A few changes to UI for the paper figures.

---
 vscode-extension/package-lock.json            |   28 +-
 vscode-extension/package.json                 |    4 +
 vscode-extension/webview-ui/package-lock.json | 7811 ++++++++++++++---
 vscode-extension/webview-ui/package.json      |    7 +-
 vscode-extension/webview-ui/src/App.tsx       |    8 +-
 .../webview-ui/src/ShowDebuggedExample.tsx    |  106 +-
 vscode-extension/webview-ui/src/tools.tsx     |    2 +-
 7 files changed, 6691 insertions(+), 1275 deletions(-)

diff --git a/vscode-extension/package-lock.json b/vscode-extension/package-lock.json
index 8b2722c..c35d7a0 100644
--- a/vscode-extension/package-lock.json
+++ b/vscode-extension/package-lock.json
@@ -324,11 +324,11 @@
       "dev": true
     },
     "node_modules/@types/node": {
-      "version": "22.0.2",
-      "resolved": "https://registry.npmjs.org/@types/node/-/node-22.0.2.tgz",
-      "integrity": "sha512-yPL6DyFwY5PiMVEwymNeqUTKsDczQBJ/5T7W/46RwLU/VH+AA8aT5TZkvBviLKLbbm0hlfftEkGrNzfRk/fofQ==",
+      "version": "22.19.15",
+      "resolved": "https://registry.npmjs.org/@types/node/-/node-22.19.15.tgz",
+      "integrity": "sha512-F0R/h2+dsy5wJAUe3tAU6oqa2qbWY5TpNfL/RGmo1y38hiyO1w3x2jPtt76wmuaJI4DQnOBu21cNXQ2STIUUWg==",
       "dependencies": {
-        "undici-types": "~6.11.1"
+        "undici-types": "~6.21.0"
       }
     },
     "node_modules/@types/node-fetch": {
@@ -3143,9 +3143,9 @@
       }
     },
     "node_modules/undici-types": {
-      "version": "6.11.1",
-      "resolved": "https://registry.npmjs.org/undici-types/-/undici-types-6.11.1.tgz",
-      "integrity": "sha512-mIDEX2ek50x0OlRgxryxsenE5XaQD4on5U2inY7RApK3SOJpofyw7uW2AyfMKkhAxXIceo2DeWGVGwyvng1GNQ=="
+      "version": "6.21.0",
+      "resolved": "https://registry.npmjs.org/undici-types/-/undici-types-6.21.0.tgz",
+      "integrity": "sha512-iwDZqg0QAGrg9Rav5H4n0M64c3mkR59cJ6wQp+7C4nI0gsmExaedaYLNO44eT4AtBBwjbTiGPMlt2Md0T9H9JQ=="
     },
     "node_modules/unpipe": {
       "version": "1.0.0",
@@ -3548,11 +3548,11 @@
       "dev": true
     },
     "@types/node": {
-      "version": "22.0.2",
-      "resolved": "https://registry.npmjs.org/@types/node/-/node-22.0.2.tgz",
-      "integrity": "sha512-yPL6DyFwY5PiMVEwymNeqUTKsDczQBJ/5T7W/46RwLU/VH+AA8aT5TZkvBviLKLbbm0hlfftEkGrNzfRk/fofQ==",
+      "version": "22.19.15",
+      "resolved": "https://registry.npmjs.org/@types/node/-/node-22.19.15.tgz",
+      "integrity": "sha512-F0R/h2+dsy5wJAUe3tAU6oqa2qbWY5TpNfL/RGmo1y38hiyO1w3x2jPtt76wmuaJI4DQnOBu21cNXQ2STIUUWg==",
       "requires": {
-        "undici-types": "~6.11.1"
+        "undici-types": "~6.21.0"
       }
     },
     "@types/node-fetch": {
@@ -5549,9 +5549,9 @@
       "dev": true
     },
     "undici-types": {
-      "version": "6.11.1",
-      "resolved": "https://registry.npmjs.org/undici-types/-/undici-types-6.11.1.tgz",
-      "integrity": "sha512-mIDEX2ek50x0OlRgxryxsenE5XaQD4on5U2inY7RApK3SOJpofyw7uW2AyfMKkhAxXIceo2DeWGVGwyvng1GNQ=="
+      "version": "6.21.0",
+      "resolved": "https://registry.npmjs.org/undici-types/-/undici-types-6.21.0.tgz",
+      "integrity": "sha512-iwDZqg0QAGrg9Rav5H4n0M64c3mkR59cJ6wQp+7C4nI0gsmExaedaYLNO44eT4AtBBwjbTiGPMlt2Md0T9H9JQ=="
     },
     "unpipe": {
       "version": "1.0.0",
diff --git a/vscode-extension/package.json b/vscode-extension/package.json
index 18f7547..443355d 100644
--- a/vscode-extension/package.json
+++ b/vscode-extension/package.json
@@ -46,6 +46,10 @@
       {
         "command": "codetations.moveSelected",
         "title": "Codetations: Move Selected"
+      },
+      {
+        "command": "codetations.setAnnotationColor",
+        "title": "Codetations: Set Annotation Color"
       }
     ],
     "menus": {
diff --git a/vscode-extension/webview-ui/package-lock.json b/vscode-extension/webview-ui/package-lock.json
index 90d97a8..75a2178 100644
--- a/vscode-extension/webview-ui/package-lock.json
+++ b/vscode-extension/webview-ui/package-lock.json
@@ -8,6 +8,11 @@
       "name": "codetations",
       "version": "0.0.1",
       "dependencies": {
+        "@tiptap/extension-image": "^3.20.5",
+        "@tiptap/extension-placeholder": "^3.20.5",
+        "@tiptap/react": "^3.20.5",
+        "@tiptap/starter-kit": "^3.20.5",
+        "@uiw/react-md-editor": "^4.0.11",
         "@vscode/webview-ui-toolkit": "^1.2.2",
         "codetations": "file:",
         "react": "^18.2.0",
@@ -22,7 +27,7 @@
         "@types/vscode-webview": "^1.57.0",
         "@vitejs/plugin-react": "^1.0.7",
         "typescript": "^4.4.4",
-        "vite": "^2.9.13"
+        "vite": "^6.4.1"
       }
     },
     "node_modules/@babel/code-frame": {
@@ -371,6 +376,14 @@
         "@babel/core": "^7.0.0-0"
       }
     },
+    "node_modules/@babel/runtime": {
+      "version": "7.29.2",
+      "resolved": "https://registry.npmjs.org/@babel/runtime/-/runtime-7.29.2.tgz",
+      "integrity": "sha512-JiDShH45zKHWyGe4ZNVRrCjBz8Nh9TMmZG1kh4QTK8hCBTWBi8Da+i7s1fJw7/lYpM4ccepSNfqzZ/QvABBi5g==",
+      "engines": {
+        "node": ">=6.9.0"
+      }
+    },
     "node_modules/@babel/template": {
       "version": "7.16.7",
       "resolved": "https://registry.npmjs.org/@babel/template/-/template-7.16.7.tgz",
@@ -419,617 +432,661 @@
         "node": ">=6.9.0"
       }
     },
-    "node_modules/@esbuild/linux-loong64": {
-      "version": "0.14.54",
-      "resolved": "https://registry.npmjs.org/@esbuild/linux-loong64/-/linux-loong64-0.14.54.tgz",
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+    "node_modules/@esbuild/aix-ppc64": {
+      "version": "0.25.12",
+      "resolved": "https://registry.npmjs.org/@esbuild/aix-ppc64/-/aix-ppc64-0.25.12.tgz",
+      "integrity": "sha512-Hhmwd6CInZ3dwpuGTF8fJG6yoWmsToE+vYgD4nytZVxcu1ulHpUQRAB1UJ8+N1Am3Mz4+xOByoQoSZf4D+CpkA==",
       "cpu": [
-        "loong64"
+        "ppc64"
       ],
       "dev": true,
       "optional": true,
       "os": [
-        "linux"
+        "aix"
       ],
       "engines": {
-        "node": ">=12"
-      }
-    },
-    "node_modules/@microsoft/fast-element": {
-      "version": "1.11.0",
-      "resolved": "https://registry.npmjs.org/@microsoft/fast-element/-/fast-element-1.11.0.tgz",
-      "integrity": "sha512-VKJYMkS5zgzHHb66sY7AFpYv6IfFhXrjQcAyNgi2ivD65My1XOhtjfKez5ELcLFRJfgZNAxvI8kE69apXERTkw=="
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-    "node_modules/@microsoft/fast-foundation": {
-      "version": "2.47.0",
-      "resolved": "https://registry.npmjs.org/@microsoft/fast-foundation/-/fast-foundation-2.47.0.tgz",
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-        "@microsoft/fast-element": "^1.11.0",
-        "@microsoft/fast-web-utilities": "^5.4.1",
-        "tabbable": "^5.2.0",
-        "tslib": "^1.13.0"
+        "node": ">=18"
       }
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-    "node_modules/@microsoft/fast-react-wrapper": {
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-        "@microsoft/fast-foundation": "^2.41.1"
-      },
-      "peerDependencies": {
-        "react": ">=16.9.0"
+    "node_modules/@esbuild/android-arm": {
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+    },
+    "rehype-stringify": {
+      "version": "10.0.1",
+      "resolved": "https://registry.npmjs.org/rehype-stringify/-/rehype-stringify-10.0.1.tgz",
+      "integrity": "sha512-k9ecfXHmIPuFVI61B9DeLPN0qFHfawM6RsuX48hoqlaKSF61RskNjSm1lI8PhBEM0MRdLxVVm4WmTqJQccH9mA==",
+      "requires": {
+        "@types/hast": "^3.0.0",
+        "hast-util-to-html": "^9.0.0",
+        "unified": "^11.0.0"
+      }
+    },
+    "remark-gfm": {
+      "version": "4.0.1",
+      "resolved": "https://registry.npmjs.org/remark-gfm/-/remark-gfm-4.0.1.tgz",
+      "integrity": "sha512-1quofZ2RQ9EWdeN34S79+KExV1764+wCUGop5CPL1WGdD0ocPpu91lzPGbwWMECpEpd42kJGQwzRfyov9j4yNg==",
+      "requires": {
+        "@types/mdast": "^4.0.0",
+        "mdast-util-gfm": "^3.0.0",
+        "micromark-extension-gfm": "^3.0.0",
+        "remark-parse": "^11.0.0",
+        "remark-stringify": "^11.0.0",
+        "unified": "^11.0.0"
+      }
+    },
+    "remark-github-blockquote-alert": {
+      "version": "1.3.1",
+      "resolved": "https://registry.npmjs.org/remark-github-blockquote-alert/-/remark-github-blockquote-alert-1.3.1.tgz",
+      "integrity": "sha512-OPNnimcKeozWN1w8KVQEuHOxgN3L4rah8geMOLhA5vN9wITqU4FWD+G26tkEsCGHiOVDbISx+Se5rGZ+D1p0Jg==",
+      "requires": {
+        "unist-util-visit": "^5.0.0"
+      }
+    },
     "remark-parse": {
       "version": "11.0.0",
       "resolved": "https://registry.npmjs.org/remark-parse/-/remark-parse-11.0.0.tgz",
@@ -5766,6 +11060,16 @@
         "vfile": "^6.0.0"
       }
     },
+    "remark-stringify": {
+      "version": "11.0.0",
+      "resolved": "https://registry.npmjs.org/remark-stringify/-/remark-stringify-11.0.0.tgz",
+      "integrity": "sha512-1OSmLd3awB/t8qdoEOMazZkNsfVTeY4fTsgzcQFdXNq8ToTN4ZGwrMnlda4K6smTFKD+GRV6O48i6Z4iKgPPpw==",
+      "requires": {
+        "@types/mdast": "^4.0.0",
+        "mdast-util-to-markdown": "^2.0.0",
+        "unified": "^11.0.0"
+      }
+    },
     "resolve": {
       "version": "1.22.1",
       "resolved": "https://registry.npmjs.org/resolve/-/resolve-1.22.1.tgz",
@@ -5778,14 +11082,45 @@
       }
     },
     "rollup": {
-      "version": "2.63.0",
-      "resolved": "https://registry.npmjs.org/rollup/-/rollup-2.63.0.tgz",
-      "integrity": "sha512-nps0idjmD+NXl6OREfyYXMn/dar3WGcyKn+KBzPdaLecub3x/LrId0wUcthcr8oZUAcZAR8NKcfGGFlNgGL1kQ==",
+      "version": "4.60.0",
+      "resolved": "https://registry.npmjs.org/rollup/-/rollup-4.60.0.tgz",
+      "integrity": "sha512-yqjxruMGBQJ2gG4HtjZtAfXArHomazDHoFwFFmZZl0r7Pdo7qCIXKqKHZc8yeoMgzJJ+pO6pEEHa+V7uzWlrAQ==",
       "dev": true,
       "requires": {
+        "@rollup/rollup-android-arm-eabi": "4.60.0",
+        "@rollup/rollup-android-arm64": "4.60.0",
+        "@rollup/rollup-darwin-arm64": "4.60.0",
+        "@rollup/rollup-darwin-x64": "4.60.0",
+        "@rollup/rollup-freebsd-arm64": "4.60.0",
+        "@rollup/rollup-freebsd-x64": "4.60.0",
+        "@rollup/rollup-linux-arm-gnueabihf": "4.60.0",
+        "@rollup/rollup-linux-arm-musleabihf": "4.60.0",
+        "@rollup/rollup-linux-arm64-gnu": "4.60.0",
+        "@rollup/rollup-linux-arm64-musl": "4.60.0",
+        "@rollup/rollup-linux-loong64-gnu": "4.60.0",
+        "@rollup/rollup-linux-loong64-musl": "4.60.0",
+        "@rollup/rollup-linux-ppc64-gnu": "4.60.0",
+        "@rollup/rollup-linux-ppc64-musl": "4.60.0",
+        "@rollup/rollup-linux-riscv64-gnu": "4.60.0",
+        "@rollup/rollup-linux-riscv64-musl": "4.60.0",
+        "@rollup/rollup-linux-s390x-gnu": "4.60.0",
+        "@rollup/rollup-linux-x64-gnu": "4.60.0",
+        "@rollup/rollup-linux-x64-musl": "4.60.0",
+        "@rollup/rollup-openbsd-x64": "4.60.0",
+        "@rollup/rollup-openharmony-arm64": "4.60.0",
+        "@rollup/rollup-win32-arm64-msvc": "4.60.0",
+        "@rollup/rollup-win32-ia32-msvc": "4.60.0",
+        "@rollup/rollup-win32-x64-gnu": "4.60.0",
+        "@rollup/rollup-win32-x64-msvc": "4.60.0",
+        "@types/estree": "1.0.8",
         "fsevents": "~2.3.2"
       }
     },
+    "rope-sequence": {
+      "version": "1.3.4",
+      "resolved": "https://registry.npmjs.org/rope-sequence/-/rope-sequence-1.3.4.tgz",
+      "integrity": "sha512-UT5EDe2cu2E/6O4igUr5PSFs23nvvukicWHx6GnOPlHAiiYbzNuCRQCuiUdHJQcqKalLKlrYJnjY0ySGsXNQXQ=="
+    },
     "safe-buffer": {
       "version": "5.1.2",
       "resolved": "https://registry.npmjs.org/safe-buffer/-/safe-buffer-5.1.2.tgz",
@@ -5813,9 +11148,9 @@
       "dev": true
     },
     "source-map-js": {
-      "version": "1.0.2",
-      "resolved": "https://registry.npmjs.org/source-map-js/-/source-map-js-1.0.2.tgz",
-      "integrity": "sha512-R0XvVJ9WusLiqTCEiGCmICCMplcCkIwwR11mOSD9CR5u+IXYdiseeEuXCVAjS54zqwkLcPNnmU4OeJ6tUrWhDw==",
+      "version": "1.2.1",
+      "resolved": "https://registry.npmjs.org/source-map-js/-/source-map-js-1.2.1.tgz",
+      "integrity": "sha512-UXWMKhLOwVKb728IUtQPXxfYU+usdybtUrK/8uGE8CQMvrhOpwvzDBwj0QhSL7MQc7vIsISBG8VQ8+IDQxpfQA==",
       "dev": true
     },
     "space-separated-tokens": {
@@ -5860,6 +11195,31 @@
       "resolved": "https://registry.npmjs.org/tabbable/-/tabbable-5.3.3.tgz",
       "integrity": "sha512-QD9qKY3StfbZqWOPLp0++pOrAVb/HbUi5xCc8cUo4XjP19808oaMiDzn0leBY5mCespIBM0CIZePzZjgzR83kA=="
     },
+    "tinyglobby": {
+      "version": "0.2.15",
+      "resolved": "https://registry.npmjs.org/tinyglobby/-/tinyglobby-0.2.15.tgz",
+      "integrity": "sha512-j2Zq4NyQYG5XMST4cbs02Ak8iJUdxRM0XI5QyxXuZOzKOINmWurp3smXu3y5wDcJrptwpSjgXHzIQxR0omXljQ==",
+      "dev": true,
+      "requires": {
+        "fdir": "^6.5.0",
+        "picomatch": "^4.0.3"
+      },
+      "dependencies": {
+        "fdir": {
+          "version": "6.5.0",
+          "resolved": "https://registry.npmjs.org/fdir/-/fdir-6.5.0.tgz",
+          "integrity": "sha512-tIbYtZbucOs0BRGqPJkshJUYdL+SDH7dVM8gjy+ERp3WAUjLEFJE+02kanyHtwjWOnwrKYBiwAmM0p4kLJAnXg==",
+          "dev": true,
+          "requires": {}
+        },
+        "picomatch": {
+          "version": "4.0.4",
+          "resolved": "https://registry.npmjs.org/picomatch/-/picomatch-4.0.4.tgz",
+          "integrity": "sha512-QP88BAKvMam/3NxH6vj2o21R6MjxZUAd6nlwAS/pnGvN9IVLocLHxGYIzFhg6fUQ+5th6P4dv4eW9jX3DSIj7A==",
+          "dev": true
+        }
+      }
+    },
     "to-fast-properties": {
       "version": "2.0.0",
       "resolved": "https://registry.npmjs.org/to-fast-properties/-/to-fast-properties-2.0.0.tgz",
@@ -5887,6 +11247,11 @@
       "integrity": "sha512-VgYs2A2QIRuGphtzFV7aQJduJ2gyfTljngLzjpfW9FoYZF6xuw1W0vW9ghCKLfcWrCFxK81CSGRAvS1pn4fIUg==",
       "dev": true
     },
+    "uc.micro": {
+      "version": "2.1.0",
+      "resolved": "https://registry.npmjs.org/uc.micro/-/uc.micro-2.1.0.tgz",
+      "integrity": "sha512-ARDJmphmdvUk6Glw7y9DQ2bFkKBHwQHLi2lsaH6PPmz/Ka9sFOBsBluozhDltWmnv9u/cF6Rt87znRTPV+yp/A=="
+    },
     "unified": {
       "version": "11.0.5",
       "resolved": "https://registry.npmjs.org/unified/-/unified-11.0.5.tgz",
@@ -5901,6 +11266,16 @@
         "vfile": "^6.0.0"
       }
     },
+    "unist-util-filter": {
+      "version": "5.0.1",
+      "resolved": "https://registry.npmjs.org/unist-util-filter/-/unist-util-filter-5.0.1.tgz",
+      "integrity": "sha512-pHx7D4Zt6+TsfwylH9+lYhBhzyhEnCXs/lbq/Hstxno5z4gVdyc2WEW0asfjGKPyG4pEKrnBv5hdkO6+aRnQJw==",
+      "requires": {
+        "@types/unist": "^3.0.0",
+        "unist-util-is": "^6.0.0",
+        "unist-util-visit-parents": "^6.0.0"
+      }
+    },
     "unist-util-is": {
       "version": "6.0.0",
       "resolved": "https://registry.npmjs.org/unist-util-is/-/unist-util-is-6.0.0.tgz",
@@ -5953,6 +11328,12 @@
         "unist-util-is": "^6.0.0"
       }
     },
+    "use-sync-external-store": {
+      "version": "1.6.0",
+      "resolved": "https://registry.npmjs.org/use-sync-external-store/-/use-sync-external-store-1.6.0.tgz",
+      "integrity": "sha512-Pp6GSwGP/NrPIrxVFAIkOQeyw8lFenOHijQWkUTrDvrF4ALqylP2C/KCkeS9dpUM3KvYRQhna5vt7IL95+ZQ9w==",
+      "requires": {}
+    },
     "vfile": {
       "version": "6.0.2",
       "resolved": "https://registry.npmjs.org/vfile/-/vfile-6.0.2.tgz",
@@ -5963,6 +11344,15 @@
         "vfile-message": "^4.0.0"
       }
     },
+    "vfile-location": {
+      "version": "5.0.3",
+      "resolved": "https://registry.npmjs.org/vfile-location/-/vfile-location-5.0.3.tgz",
+      "integrity": "sha512-5yXvWDEgqeiYiBe1lbxYF7UMAIm/IcopxMHrMQDq3nvKcjPKIhZklUKL+AE7J7uApI4kwe2snsK+eI6UTj9EHg==",
+      "requires": {
+        "@types/unist": "^3.0.0",
+        "vfile": "^6.0.0"
+      }
+    },
     "vfile-message": {
       "version": "4.0.2",
       "resolved": "https://registry.npmjs.org/vfile-message/-/vfile-message-4.0.2.tgz",
@@ -5973,18 +11363,45 @@
       }
     },
     "vite": {
-      "version": "2.9.13",
-      "resolved": "https://registry.npmjs.org/vite/-/vite-2.9.13.tgz",
-      "integrity": "sha512-AsOBAaT0AD7Mhe8DuK+/kE4aWYFMx/i0ZNi98hJclxb4e0OhQcZYUrvLjIaQ8e59Ui7txcvKMiJC1yftqpQoDw==",
+      "version": "6.4.1",
+      "resolved": "https://registry.npmjs.org/vite/-/vite-6.4.1.tgz",
+      "integrity": "sha512-+Oxm7q9hDoLMyJOYfUYBuHQo+dkAloi33apOPP56pzj+vsdJDzr+j1NISE5pyaAuKL4A3UD34qd0lx5+kfKp2g==",
       "dev": true,
       "requires": {
-        "esbuild": "^0.14.27",
-        "fsevents": "~2.3.2",
-        "postcss": "^8.4.13",
-        "resolve": "^1.22.0",
-        "rollup": "^2.59.0"
+        "esbuild": "^0.25.0",
+        "fdir": "^6.4.4",
+        "fsevents": "~2.3.3",
+        "picomatch": "^4.0.2",
+        "postcss": "^8.5.3",
+        "rollup": "^4.34.9",
+        "tinyglobby": "^0.2.13"
+      },
+      "dependencies": {
+        "fdir": {
+          "version": "6.5.0",
+          "resolved": "https://registry.npmjs.org/fdir/-/fdir-6.5.0.tgz",
+          "integrity": "sha512-tIbYtZbucOs0BRGqPJkshJUYdL+SDH7dVM8gjy+ERp3WAUjLEFJE+02kanyHtwjWOnwrKYBiwAmM0p4kLJAnXg==",
+          "dev": true,
+          "requires": {}
+        },
+        "picomatch": {
+          "version": "4.0.4",
+          "resolved": "https://registry.npmjs.org/picomatch/-/picomatch-4.0.4.tgz",
+          "integrity": "sha512-QP88BAKvMam/3NxH6vj2o21R6MjxZUAd6nlwAS/pnGvN9IVLocLHxGYIzFhg6fUQ+5th6P4dv4eW9jX3DSIj7A==",
+          "dev": true
+        }
       }
     },
+    "w3c-keyname": {
+      "version": "2.2.8",
+      "resolved": "https://registry.npmjs.org/w3c-keyname/-/w3c-keyname-2.2.8.tgz",
+      "integrity": "sha512-dpojBhNsCNN7T82Tm7k26A6G9ML3NkhDsnw9n/eoxSRlVBB4CEtIQ/KTCLI2Fwf3ataSXRhYFkQi3SlnFwPvPQ=="
+    },
+    "web-namespaces": {
+      "version": "2.0.1",
+      "resolved": "https://registry.npmjs.org/web-namespaces/-/web-namespaces-2.0.1.tgz",
+      "integrity": "sha512-bKr1DkiNa2krS7qxNtdrtHAmzuYGFQLiQ13TsorsdT6ULTkPLKuu5+GsFpDlg6JFjUTwX2DyhMPG2be8uPrqsQ=="
+    },
     "zwitch": {
       "version": "2.0.4",
       "resolved": "https://registry.npmjs.org/zwitch/-/zwitch-2.0.4.tgz",
diff --git a/vscode-extension/webview-ui/package.json b/vscode-extension/webview-ui/package.json
index e52b50a..35d36a1 100644
--- a/vscode-extension/webview-ui/package.json
+++ b/vscode-extension/webview-ui/package.json
@@ -9,6 +9,11 @@
     "preview": "vite preview"
   },
   "dependencies": {
+    "@tiptap/extension-image": "^3.20.5",
+    "@tiptap/extension-placeholder": "^3.20.5",
+    "@tiptap/react": "^3.20.5",
+    "@tiptap/starter-kit": "^3.20.5",
+    "@uiw/react-md-editor": "^4.0.11",
     "@vscode/webview-ui-toolkit": "^1.2.2",
     "codetations": "file:",
     "react": "^18.2.0",
@@ -23,6 +28,6 @@
     "@types/vscode-webview": "^1.57.0",
     "@vitejs/plugin-react": "^1.0.7",
     "typescript": "^4.4.4",
-    "vite": "^2.9.13"
+    "vite": "^6.4.1"
   }
 }
diff --git a/vscode-extension/webview-ui/src/App.tsx b/vscode-extension/webview-ui/src/App.tsx
index 05e9390..b607172 100644
--- a/vscode-extension/webview-ui/src/App.tsx
+++ b/vscode-extension/webview-ui/src/App.tsx
@@ -427,10 +427,10 @@ function App() {
 
     // Check for overlapping annotations
     for (let i = 0; i < annotations.length; i++) {
-      if (annotations[i].start === start && annotations[i].end === end) {
-        showErrorMessage("Error adding annotations: annotation already exists in selected area");
-        return;
-      }
+      // if (annotations[i].start === start && annotations[i].end === end) {
+      //   showErrorMessage("Error adding annotations: annotation already exists in selected area");
+      //   return;
+      // }
     }
 
     // Pick a colorblind-friendly annotation color, rotating through a list
diff --git a/vscode-extension/webview-ui/src/ShowDebuggedExample.tsx b/vscode-extension/webview-ui/src/ShowDebuggedExample.tsx
index 3aa7425..ee43541 100644
--- a/vscode-extension/webview-ui/src/ShowDebuggedExample.tsx
+++ b/vscode-extension/webview-ui/src/ShowDebuggedExample.tsx
@@ -263,50 +263,6 @@ Focus on making the code runnable in a browser JavaScript environment without an
   return (
     <div style={{ padding: "10px", fontFamily: "Poppins, sans-serif" }}>
       <div style={{ marginBottom: "12px" }}>
-        <div style={{ 
-          display: "flex", 
-          justifyContent: "space-between", 
-          alignItems: "center",
-          marginBottom: "8px"
-        }}>
-          <label style={{ fontWeight: "bold", fontSize: "14px" }}>
-            Debug Example Code:
-          </label>
-          <div>
-            <button
-              onClick={generateDebugCode}
-              disabled={isGenerating}
-              style={{
-                padding: "6px 12px",
-                backgroundColor: isGenerating ? "#cccccc" : "#0078D4",
-                color: "white",
-                border: "none",
-                borderRadius: "4px",
-                cursor: isGenerating ? "default" : "pointer",
-                fontSize: "14px",
-                marginRight: "8px"
-              }}
-            >
-              {isGenerating ? "Generating..." : "Regenerate"}
-            </button>
-            <button
-              onClick={executeCode}
-              disabled={isLoading || !debugCode.trim()}
-              style={{
-                padding: "6px 12px",
-                backgroundColor: isLoading ? "#cccccc" : "#107C10",
-                color: "white",
-                border: "none",
-                borderRadius: "4px",
-                cursor: isLoading ? "default" : "pointer",
-                fontSize: "14px"
-              }}
-            >
-              {isLoading ? "Executing..." : "Run Code"}
-            </button>
-          </div>
-        </div>
-        
         <div style={{ marginBottom: "10px" }}>
           <label style={{ 
             display: "block",
@@ -314,7 +270,7 @@ Focus on making the code runnable in a browser JavaScript environment without an
             fontSize: "14px",
             marginBottom: "5px"
           }}>
-            Debugging Instructions:
+            Describe the example you want to see debugged (optional):
           </label>
           <input
             type="text"
@@ -330,13 +286,28 @@ Focus on making the code runnable in a browser JavaScript environment without an
               marginBottom: "10px"
             }}
           />
-          <div style={{
+          {/* <div style={{
             fontSize: "12px",
             color: "#666",
             fontStyle: "italic"
           }}>
             Add natural language instructions to guide how the code is debugged
-          </div>
+          </div> */}
+          <button
+            onClick={generateDebugCode}
+            disabled={isGenerating}
+            style={{
+              padding: "6px 12px",
+              backgroundColor: isGenerating ? "#cccccc" : "#0078D4",
+              color: "white",
+              border: "none",
+              borderRadius: "4px",
+              cursor: isGenerating ? "default" : "pointer",
+              fontSize: "14px"
+            }}
+          >
+            {isGenerating ? "Generating..." : "Update"}
+          </button>
         </div>
         
         {explanation && (
@@ -366,6 +337,22 @@ Focus on making the code runnable in a browser JavaScript environment without an
             resize: "vertical"
           }}
         />
+        <button
+          onClick={executeCode}
+          disabled={isLoading || !debugCode.trim()}
+          style={{
+            padding: "6px 12px",
+            backgroundColor: isLoading ? "#cccccc" : "#107C10",
+            color: "white",
+            border: "none",
+            borderRadius: "4px",
+            cursor: isLoading ? "default" : "pointer",
+            fontSize: "14px",
+            marginTop: "8px"
+          }}
+        >
+          {isLoading ? "Executing..." : "Run Code"}
+        </button>
       </div>
 
       <div style={{ 
@@ -373,7 +360,7 @@ Focus on making the code runnable in a browser JavaScript environment without an
         alignItems: "center", 
         marginBottom: "8px"
       }}>
-        <label style={{ 
+        {/* <label style={{ 
           display: "flex", 
           alignItems: "center", 
           fontSize: "12px",
@@ -387,7 +374,7 @@ Focus on making the code runnable in a browser JavaScript environment without an
             style={{ marginRight: "5px" }}
           />
           Use mock API (for testing)
-        </label>
+        </label> */}
       </div>
 
       {error && (
@@ -410,16 +397,19 @@ Focus on making the code runnable in a browser JavaScript environment without an
             marginBottom: "5px", 
             fontSize: "14px",
             display: "flex",
-            alignItems: "center"
+            alignItems: "center",
+            justifyContent: "space-between"
           }}>
-            <div style={{ 
-              width: "10px", 
-              height: "10px", 
-              borderRadius: "50%", 
-              backgroundColor: executionResult.success ? "#107C10" : "#D83B01",
-              marginRight: "8px" 
-            }}></div>
-            Execution Results:
+              <div style={{ display: "flex", alignItems: "center" }}>
+              <div style={{ 
+                width: "10px", 
+                height: "10px", 
+                borderRadius: "50%", 
+                backgroundColor: executionResult.success ? "#107C10" : "#D83B01",
+                marginRight: "8px" 
+              }}></div>
+              Execution Results:
+            </div>
           </div>
           
           <div style={{ 
diff --git a/vscode-extension/webview-ui/src/tools.tsx b/vscode-extension/webview-ui/src/tools.tsx
index fd43e46..f9c09bb 100644
--- a/vscode-extension/webview-ui/src/tools.tsx
+++ b/vscode-extension/webview-ui/src/tools.tsx
@@ -363,7 +363,7 @@ export const toolNames = {
   displayHTML: "HTML Preview",
   odyssey: "Analyze Floating-point Expression",
   yesNoQuestion: "LM Unit Test",
-  debugExample: "Show Debugged Example",
+  debugExample: "Show an Example",
   explainInEnglish: "Explain in English",
   outputVisualizer: "Output Visualizer",
   formalSpecification: "Formal Specification",

From dd32d8f9a377969c28293ab1522b6aa54d45bf1a Mon Sep 17 00:00:00 2001
From: Edward Misback <misback@cs.washington.edu>
Date: Tue, 7 Apr 2026 01:00:37 -0400
Subject: [PATCH 06/22] bump version

---
 vscode-extension/package.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/vscode-extension/package.json b/vscode-extension/package.json
index 443355d..6482329 100644
--- a/vscode-extension/package.json
+++ b/vscode-extension/package.json
@@ -4,7 +4,7 @@
   "publisher": "codetations",
   "repository": "github:elmisback/codetations",
   "description": "Rich code annotations for VS Code",
-  "version": "0.0.24",
+  "version": "0.0.25",
   "engines": {
     "vscode": "^1.110.0"
   },

From cd64a07e070386cc2228003ce15cd197446ab711 Mon Sep 17 00:00:00 2001
From: Edward Misback <misback@cs.washington.edu>
Date: Tue, 7 Apr 2026 05:18:51 -0400
Subject: [PATCH 07/22] Hack in document modification.

Also add some extra logging.
---
 vscode-extension/src/AnnotationTracker.ts     | 100 +++++++++++++++---
 .../src/panels/BaseAnnotationView.ts          |   5 +-
 vscode-extension/webview-ui/src/App.tsx       |   8 +-
 3 files changed, 95 insertions(+), 18 deletions(-)

diff --git a/vscode-extension/src/AnnotationTracker.ts b/vscode-extension/src/AnnotationTracker.ts
index 64dd73b..bcba726 100644
--- a/vscode-extension/src/AnnotationTracker.ts
+++ b/vscode-extension/src/AnnotationTracker.ts
@@ -375,7 +375,9 @@ export class AnnotationTracker implements vscode.Disposable {
    * Updates the decorations in the editor
    */
   public updateDecorations(document: vscode.TextDocument): void {
+    console.log("Updating decorations for document", document.uri.toString());
     const documentKey = document.uri.toString();
+    console.log(this.documentAnnotations.get(documentKey));
     const annotations = this.documentAnnotations.get(documentKey) || [];
     
     // Clear existing decorations
@@ -524,12 +526,13 @@ export class AnnotationTracker implements vscode.Disposable {
   /**
    * Notifies the annotation panel of changed annotations
    */
-  private notifyAnnotationsChanged(document: vscode.TextDocument): void {
+  private async notifyAnnotationsChanged(document: vscode.TextDocument): Promise<void> {
+    console.log("Notifying annotation panel of changes for document", document.uri.toString());
     if (AnnotationManagerPanel.currentPanel) {
       const documentKey = document.uri.toString();
       const annotations = this.documentAnnotations.get(documentKey) || [];
       
-      AnnotationManagerPanel.currentPanel.sendMessageObject({
+      await AnnotationManagerPanel.currentPanel.sendMessageObject({
         command: "updateAnnotations",
         data: {
           documentUri: document.uri.toString(),
@@ -620,22 +623,95 @@ export class AnnotationTracker implements vscode.Disposable {
 
   /**
    * Updates an existing annotation
+   * 
+   * forces changes to wait until other document updates are processed
    */
-  public updateAnnotation(document: vscode.TextDocument, updatedAnnotation: Annotation): void {
+  public async updateAnnotation(document: vscode.TextDocument, updatedAnnotation: Annotation): Promise<void> {
+    console.log("Updating annotation", updatedAnnotation.id, "for document", document.uri.toString(), "with updated annotation", updatedAnnotation);
     const documentKey = document.uri.toString();
     const annotations = this.documentAnnotations.get(documentKey) || [];
+    const fixedUpdatedAnnotation = {
+      ...updatedAnnotation,
+      document: updatedAnnotation.document || document.getText() // Ensure the annotation's document field is updated to match the current document text
+    };
+
+    // Skip identical annotation updates to avoid wasting time on decorations and saves
+    const existingAnnotation = annotations.find(a => a.id === updatedAnnotation.id);
+    if (existingAnnotation) {
+      const isIdentical = existingAnnotation.start === fixedUpdatedAnnotation.start &&
+                          existingAnnotation.end === fixedUpdatedAnnotation.end &&
+                          existingAnnotation.document === fixedUpdatedAnnotation.document &&
+        JSON.stringify(existingAnnotation.metadata) === JSON.stringify(fixedUpdatedAnnotation.metadata);
+      if (isIdentical) {
+        console.log("Skipping annotation update because it is identical to the existing annotation");
+        return;
+      }
+    }
     
-    // Update the annotation
-    const updatedAnnotations = annotations.map(a => 
-      a.id === updatedAnnotation.id ? updatedAnnotation : a
-    );
+    // // Update the annotation
+    // const updatedAnnotations = annotations.map(a => 
+    //   a.id === updatedAnnotation.id ? fixedUpdatedAnnotation : a
+    // );
+
+    // getUpdatedAnnotations as a function
+    const getUpdatedAnnotations = (currentDocumentText: string): Annotation[] => {
+      return annotations.map(a => 
+        a.id === updatedAnnotation.id ?
+          {
+            ...a,
+            ...updatedAnnotation,
+            ...this.documentAnnotations.get(documentKey)?.find(a => a.id === updatedAnnotation.id), // Preserve any fields not included in the update
+            document: updatedAnnotation.document || currentDocumentText // Ensure the annotation's document field is updated to match the current document text
+          } 
+        : a
+      );
+    };
     
-    this.documentAnnotations.set(documentKey, updatedAnnotations);
+    this.documentAnnotations.set(documentKey, getUpdatedAnnotations(document.getText()));
+
+    await this.saveAnnotationsForDocument(document);
+
+    // If the annotation's document text has changed, we may need to update the document on disk to match the annotation's document
+    if (updatedAnnotation.document && updatedAnnotation.document !== document.getText()) {
+      console.debug("Annotation document text differs from current document text, updating document to match annotation");
+      // Update the document text to match the annotation's document
+      const edit = new vscode.WorkspaceEdit();
+      const fullRange = new vscode.Range(
+        document.positionAt(0),
+        document.positionAt(document.getText().length)
+      );
+      edit.replace(document.uri, fullRange, updatedAnnotation.document);
+      await vscode.workspace.applyEdit(edit).then(async success => {
+        if (!success) {
+          console.error("Failed to update document text to match annotation");
+
+          // Revert the annotation update if the document update fails
+          const revertedAnnotations = annotations.map(a => 
+            a.id === updatedAnnotation.id ? {...a, document: document.getText()} : a
+          );
+          this.documentAnnotations.set(documentKey, revertedAnnotations);
+          await this.updateDecorations(document);
+          await this.notifyAnnotationsChanged(document);
+          return;
+        }
+        this.documentAnnotations.set(documentKey, getUpdatedAnnotations(document.getText()));
+        await this.saveAnnotationsForDocument(document);
+        await this.updateDecorations(document);
+        await this.notifyAnnotationsChanged(document);
+        await this.updateDecorations(document);
+      });
+      console.debug("finished updating document text to match annotation for", updatedAnnotation);
+      const updatedDoc = await vscode.workspace.openTextDocument(document.uri);
+      await this.updateDecorations(updatedDoc);
+      return; // Wait for the document update to trigger the annotation update through the change listener
+      // NOTE I didn't think hard about this, it might not work as expected for unusual updates.
+    }
     
-    // Update decorations and save
-    this.updateDecorations(document);
-    this.saveAnnotationsForDocument(document);
-    this.notifyAnnotationsChanged(document);
+    // Update decorations and save, making sure decoration updates happen after document text is updated
+    await this.updateDecorations(document);
+    await this.saveAnnotationsForDocument(document);
+    await this.notifyAnnotationsChanged(document);
+    console.debug("Finished updating annotation", updatedAnnotation);
   }
 
   /**
diff --git a/vscode-extension/src/panels/BaseAnnotationView.ts b/vscode-extension/src/panels/BaseAnnotationView.ts
index 950f894..542f3fa 100644
--- a/vscode-extension/src/panels/BaseAnnotationView.ts
+++ b/vscode-extension/src/panels/BaseAnnotationView.ts
@@ -150,6 +150,7 @@ export abstract class BaseAnnotationView {
   protected _setWebviewMessageListener(webview: Webview) {
     webview.onDidReceiveMessage(
       async (message: any) => {
+        console.log("Received message from webview:", message);
         const command = message.command;
         const editor = this._getCurrentEditor();
 
@@ -402,9 +403,9 @@ export abstract class BaseAnnotationView {
   /**
    * Sends a message to the webview context.
    */
-  public sendMessageObject(message: any) {
+  public async sendMessageObject(message: any) {
     // Implement in child classes
-    this.webview.postMessage(JSON.stringify(message));
+    await this.webview.postMessage(JSON.stringify(message));
   }
   
   /**
diff --git a/vscode-extension/webview-ui/src/App.tsx b/vscode-extension/webview-ui/src/App.tsx
index b607172..320a917 100644
--- a/vscode-extension/webview-ui/src/App.tsx
+++ b/vscode-extension/webview-ui/src/App.tsx
@@ -51,7 +51,7 @@ function AnnotationEditorContainer(props: {
           },
           setMetadata: (newMetadata: any) => {
             setValue({
-              document: value.document,
+              // document: value.document,
               metadata: { ...value.metadata, ...newMetadata },
             });
           },
@@ -148,14 +148,14 @@ function AnnotationSidebarView(props: {
   };
 
   const handleAnnotationUpdate = (id: string, value: AnnotationUpdate) => {
-    console.log("Updating annotation:", id, value);
+    console.log("Webview: updating annotation:", id, value);
     
     const annotation = annotations.find(a => a.id === id);
     if (!annotation) return;
     
     const updatedAnnotation = {
       ...annotation,
-      ...(value.document ? { document: value.document } : {}),
+      ...(value.document ? { document: value.document } : {document: undefined}),
       ...(value.metadata ? { metadata: { ...annotation.metadata, ...value.metadata } } : {})
     };
     
@@ -523,7 +523,7 @@ function App() {
     // Message handler for communication with extension
     const handleMessage = (event: MessageEvent) => {
       const message = JSON.parse(event.data);
-      console.debug("Received message:", message);
+      console.debug("Webview: handleMessage: Received message:", message);
       
       switch (message.command) {
         case "initialize":

From 06a83904bebedbe2e660942c3f483138e5b8a2ba Mon Sep 17 00:00:00 2001
From: Edward Misback <misback@cs.washington.edu>
Date: Tue, 7 Apr 2026 05:19:18 -0400
Subject: [PATCH 08/22] use 5.4 mini for codegen

---
 vscode-extension/webview-ui/src/LMUnitTest.tsx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/vscode-extension/webview-ui/src/LMUnitTest.tsx b/vscode-extension/webview-ui/src/LMUnitTest.tsx
index 45c03b8..68814af 100644
--- a/vscode-extension/webview-ui/src/LMUnitTest.tsx
+++ b/vscode-extension/webview-ui/src/LMUnitTest.tsx
@@ -154,7 +154,7 @@ The "answer" field must be true or false. The "explanation" should be brief and
         // Use either the real API or the mock API based on useMock flag
         response = await (useMock ? mockLmApi : lmApi).chat(prompt, {
           vendor: 'copilot',
-          family: 'gpt-4o',
+          family: 'gpt-5.4-mini',
           temperature: 0.3
         });
         addDebugInfo("Received response from LM API");

From 0036d1a6606acf384e7191d591117425b5c6e04e Mon Sep 17 00:00:00 2001
From: Edward Misback <misback@cs.washington.edu>
Date: Tue, 7 Apr 2026 05:19:46 -0400
Subject: [PATCH 09/22] bump version

---
 vscode-extension/package.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/vscode-extension/package.json b/vscode-extension/package.json
index 6482329..2d4e8cb 100644
--- a/vscode-extension/package.json
+++ b/vscode-extension/package.json
@@ -4,7 +4,7 @@
   "publisher": "codetations",
   "repository": "github:elmisback/codetations",
   "description": "Rich code annotations for VS Code",
-  "version": "0.0.25",
+  "version": "0.0.26",
   "engines": {
     "vscode": "^1.110.0"
   },

From ae919ff057e86cbcdbe89166852cd6da9abd444d Mon Sep 17 00:00:00 2001
From: Edward Misback <misback@cs.washington.edu>
Date: Tue, 7 Apr 2026 07:24:50 -0400
Subject: [PATCH 10/22] bump version and fix build

---
 vscode-extension/package-lock.json            | 62 +++----------------
 vscode-extension/package.json                 |  2 +-
 vscode-extension/webview-ui/package-lock.json | 28 +++++++--
 vscode-extension/webview-ui/package.json      |  1 +
 4 files changed, 35 insertions(+), 58 deletions(-)

diff --git a/vscode-extension/package-lock.json b/vscode-extension/package-lock.json
index c35d7a0..94f3270 100644
--- a/vscode-extension/package-lock.json
+++ b/vscode-extension/package-lock.json
@@ -1,12 +1,12 @@
 {
   "name": "codetations",
-  "version": "0.0.24",
+  "version": "0.0.26",
   "lockfileVersion": 2,
   "requires": true,
   "packages": {
     "": {
       "name": "codetations",
-      "version": "0.0.24",
+      "version": "0.0.26",
       "dependencies": {
         "chokidar": "^3.6.0",
         "cors": "^2.8.5",
@@ -19,7 +19,7 @@
         "@types/cors": "^2.8.17",
         "@types/express": "^4.17.21",
         "@types/glob": "^7.1.3",
-        "@types/node": "^22.0.2",
+        "@types/node": "^18.11.18",
         "@types/vscode": "^1.110.0",
         "@types/ws": "^8.5.12",
         "@typescript-eslint/eslint-plugin": "^4.14.1",
@@ -324,12 +324,9 @@
       "dev": true
     },
     "node_modules/@types/node": {
-      "version": "22.19.15",
-      "resolved": "https://registry.npmjs.org/@types/node/-/node-22.19.15.tgz",
-      "integrity": "sha512-F0R/h2+dsy5wJAUe3tAU6oqa2qbWY5TpNfL/RGmo1y38hiyO1w3x2jPtt76wmuaJI4DQnOBu21cNXQ2STIUUWg==",
-      "dependencies": {
-        "undici-types": "~6.21.0"
-      }
+      "version": "18.11.18",
+      "resolved": "https://registry.npmjs.org/@types/node/-/node-18.11.18.tgz",
+      "integrity": "sha512-DHQpWGjyQKSHj3ebjFI/wRKcqQcdR+MoFBygntYOZytCqNfkd2ZC4ARDJ2DQqhjH5p85Nnd3jhUJIXrszFX/JA=="
     },
     "node_modules/@types/node-fetch": {
       "version": "2.6.11",
@@ -2422,19 +2419,6 @@
         "openai": "bin/cli"
       }
     },
-    "node_modules/openai/node_modules/@types/node": {
-      "version": "18.19.42",
-      "resolved": "https://registry.npmjs.org/@types/node/-/node-18.19.42.tgz",
-      "integrity": "sha512-d2ZFc/3lnK2YCYhos8iaNIYu9Vfhr92nHiyJHRltXWjXUBjEE+A4I58Tdbnw4VhggSW+2j5y5gTrLs4biNnubg==",
-      "dependencies": {
-        "undici-types": "~5.26.4"
-      }
-    },
-    "node_modules/openai/node_modules/undici-types": {
-      "version": "5.26.5",
-      "resolved": "https://registry.npmjs.org/undici-types/-/undici-types-5.26.5.tgz",
-      "integrity": "sha512-JlCMO+ehdEIKqlFxk6IfVoAUVmgz7cU7zD/h9XZ0qzeosSHmUJVOzSQvvYSYWXkFXC+IfLKSIffhv0sVZup6pA=="
-    },
     "node_modules/optionator": {
       "version": "0.9.1",
       "resolved": "https://registry.npmjs.org/optionator/-/optionator-0.9.1.tgz",
@@ -3142,11 +3126,6 @@
         "node": ">=4.2.0"
       }
     },
-    "node_modules/undici-types": {
-      "version": "6.21.0",
-      "resolved": "https://registry.npmjs.org/undici-types/-/undici-types-6.21.0.tgz",
-      "integrity": "sha512-iwDZqg0QAGrg9Rav5H4n0M64c3mkR59cJ6wQp+7C4nI0gsmExaedaYLNO44eT4AtBBwjbTiGPMlt2Md0T9H9JQ=="
-    },
     "node_modules/unpipe": {
       "version": "1.0.0",
       "resolved": "https://registry.npmjs.org/unpipe/-/unpipe-1.0.0.tgz",
@@ -3548,12 +3527,9 @@
       "dev": true
     },
     "@types/node": {
-      "version": "22.19.15",
-      "resolved": "https://registry.npmjs.org/@types/node/-/node-22.19.15.tgz",
-      "integrity": "sha512-F0R/h2+dsy5wJAUe3tAU6oqa2qbWY5TpNfL/RGmo1y38hiyO1w3x2jPtt76wmuaJI4DQnOBu21cNXQ2STIUUWg==",
-      "requires": {
-        "undici-types": "~6.21.0"
-      }
+      "version": "18.11.18",
+      "resolved": "https://registry.npmjs.org/@types/node/-/node-18.11.18.tgz",
+      "integrity": "sha512-DHQpWGjyQKSHj3ebjFI/wRKcqQcdR+MoFBygntYOZytCqNfkd2ZC4ARDJ2DQqhjH5p85Nnd3jhUJIXrszFX/JA=="
     },
     "@types/node-fetch": {
       "version": "2.6.11",
@@ -5040,21 +5016,6 @@
         "form-data-encoder": "1.7.2",
         "formdata-node": "^4.3.2",
         "node-fetch": "^2.6.7"
-      },
-      "dependencies": {
-        "@types/node": {
-          "version": "18.19.42",
-          "resolved": "https://registry.npmjs.org/@types/node/-/node-18.19.42.tgz",
-          "integrity": "sha512-d2ZFc/3lnK2YCYhos8iaNIYu9Vfhr92nHiyJHRltXWjXUBjEE+A4I58Tdbnw4VhggSW+2j5y5gTrLs4biNnubg==",
-          "requires": {
-            "undici-types": "~5.26.4"
-          }
-        },
-        "undici-types": {
-          "version": "5.26.5",
-          "resolved": "https://registry.npmjs.org/undici-types/-/undici-types-5.26.5.tgz",
-          "integrity": "sha512-JlCMO+ehdEIKqlFxk6IfVoAUVmgz7cU7zD/h9XZ0qzeosSHmUJVOzSQvvYSYWXkFXC+IfLKSIffhv0sVZup6pA=="
-        }
       }
     },
     "optionator": {
@@ -5548,11 +5509,6 @@
       "integrity": "sha512-1FXk9E2Hm+QzZQ7z+McJiHL4NW1F2EzMu9Nq9i3zAaGqibafqYwCVU6WyWAuyQRRzOlxou8xZSyXLEN8oKj24g==",
       "dev": true
     },
-    "undici-types": {
-      "version": "6.21.0",
-      "resolved": "https://registry.npmjs.org/undici-types/-/undici-types-6.21.0.tgz",
-      "integrity": "sha512-iwDZqg0QAGrg9Rav5H4n0M64c3mkR59cJ6wQp+7C4nI0gsmExaedaYLNO44eT4AtBBwjbTiGPMlt2Md0T9H9JQ=="
-    },
     "unpipe": {
       "version": "1.0.0",
       "resolved": "https://registry.npmjs.org/unpipe/-/unpipe-1.0.0.tgz",
diff --git a/vscode-extension/package.json b/vscode-extension/package.json
index 2d4e8cb..0c7079a 100644
--- a/vscode-extension/package.json
+++ b/vscode-extension/package.json
@@ -4,7 +4,7 @@
   "publisher": "codetations",
   "repository": "github:elmisback/codetations",
   "description": "Rich code annotations for VS Code",
-  "version": "0.0.26",
+  "version": "0.0.27",
   "engines": {
     "vscode": "^1.110.0"
   },
diff --git a/vscode-extension/webview-ui/package-lock.json b/vscode-extension/webview-ui/package-lock.json
index 75a2178..cbc7025 100644
--- a/vscode-extension/webview-ui/package-lock.json
+++ b/vscode-extension/webview-ui/package-lock.json
@@ -22,6 +22,7 @@
         "react-markdown": "^9.0.1"
       },
       "devDependencies": {
+        "@types/node": "^18.11.18",
         "@types/react": "^18.0.0",
         "@types/react-dom": "^18.0.0",
         "@types/vscode-webview": "^1.57.0",
@@ -1743,6 +1744,12 @@
       "resolved": "https://registry.npmjs.org/@types/ms/-/ms-0.7.34.tgz",
       "integrity": "sha512-nG96G3Wp6acyAgJqGasjODb+acrI7KltPiRxzHPXnP3NgI28bpQDRv53olbqGXbfcgF5aiiHmO3xpwEpS5Ld9g=="
     },
+    "node_modules/@types/node": {
+      "version": "18.11.18",
+      "resolved": "https://registry.npmjs.org/@types/node/-/node-18.11.18.tgz",
+      "integrity": "sha512-DHQpWGjyQKSHj3ebjFI/wRKcqQcdR+MoFBygntYOZytCqNfkd2ZC4ARDJ2DQqhjH5p85Nnd3jhUJIXrszFX/JA==",
+      "dev": true
+    },
     "node_modules/@types/prismjs": {
       "version": "1.26.6",
       "resolved": "https://registry.npmjs.org/@types/prismjs/-/prismjs-1.26.6.tgz",
@@ -5939,6 +5946,12 @@
       "resolved": "https://registry.npmjs.org/@types/ms/-/ms-0.7.34.tgz",
       "integrity": "sha512-nG96G3Wp6acyAgJqGasjODb+acrI7KltPiRxzHPXnP3NgI28bpQDRv53olbqGXbfcgF5aiiHmO3xpwEpS5Ld9g=="
     },
+    "@types/node": {
+      "version": "18.11.18",
+      "resolved": "https://registry.npmjs.org/@types/node/-/node-18.11.18.tgz",
+      "integrity": "sha512-DHQpWGjyQKSHj3ebjFI/wRKcqQcdR+MoFBygntYOZytCqNfkd2ZC4ARDJ2DQqhjH5p85Nnd3jhUJIXrszFX/JA==",
+      "dev": true
+    },
     "@types/prismjs": {
       "version": "1.26.6",
       "resolved": "https://registry.npmjs.org/@types/prismjs/-/prismjs-1.26.6.tgz",
@@ -6200,10 +6213,11 @@
     "codetations": {
       "version": "file:",
       "requires": {
-        "@tiptap/extension-image": "*",
-        "@tiptap/extension-placeholder": "*",
-        "@tiptap/react": "*",
-        "@tiptap/starter-kit": "*",
+        "@tiptap/extension-image": "^3.20.5",
+        "@tiptap/extension-placeholder": "^3.20.5",
+        "@tiptap/react": "^3.20.5",
+        "@tiptap/starter-kit": "^3.20.5",
+        "@types/node": "18.11.18",
         "@types/react": "^18.0.0",
         "@types/react-dom": "^18.0.0",
         "@types/vscode-webview": "^1.57.0",
@@ -7237,6 +7251,12 @@
           "resolved": "https://registry.npmjs.org/@types/ms/-/ms-0.7.34.tgz",
           "integrity": "sha512-nG96G3Wp6acyAgJqGasjODb+acrI7KltPiRxzHPXnP3NgI28bpQDRv53olbqGXbfcgF5aiiHmO3xpwEpS5Ld9g=="
         },
+        "@types/node": {
+          "version": "18.11.18",
+          "resolved": "https://registry.npmjs.org/@types/node/-/node-18.11.18.tgz",
+          "integrity": "sha512-DHQpWGjyQKSHj3ebjFI/wRKcqQcdR+MoFBygntYOZytCqNfkd2ZC4ARDJ2DQqhjH5p85Nnd3jhUJIXrszFX/JA==",
+          "dev": true
+        },
         "@types/prismjs": {
           "version": "1.26.6",
           "resolved": "https://registry.npmjs.org/@types/prismjs/-/prismjs-1.26.6.tgz",
diff --git a/vscode-extension/webview-ui/package.json b/vscode-extension/webview-ui/package.json
index 35d36a1..9202628 100644
--- a/vscode-extension/webview-ui/package.json
+++ b/vscode-extension/webview-ui/package.json
@@ -23,6 +23,7 @@
     "react-markdown": "^9.0.1"
   },
   "devDependencies": {
+    "@types/node": "^18.11.18",
     "@types/react": "^18.0.0",
     "@types/react-dom": "^18.0.0",
     "@types/vscode-webview": "^1.57.0",

From 5e3e1f605e75cd8880e7e278957cf2960e3d38a6 Mon Sep 17 00:00:00 2001
From: Edward Misback <misback@cs.washington.edu>
Date: Wed, 8 Apr 2026 20:37:47 -0400
Subject: [PATCH 11/22] Fix nasty retag bug introduced by doc mods.

---
 vscode-extension/src/AnnotationTracker.ts | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/vscode-extension/src/AnnotationTracker.ts b/vscode-extension/src/AnnotationTracker.ts
index bcba726..4e39354 100644
--- a/vscode-extension/src/AnnotationTracker.ts
+++ b/vscode-extension/src/AnnotationTracker.ts
@@ -655,12 +655,12 @@ export class AnnotationTracker implements vscode.Disposable {
 
     // getUpdatedAnnotations as a function
     const getUpdatedAnnotations = (currentDocumentText: string): Annotation[] => {
+      const annotations = this.documentAnnotations.get(documentKey) || [];
       return annotations.map(a => 
         a.id === updatedAnnotation.id ?
           {
             ...a,
             ...updatedAnnotation,
-            ...this.documentAnnotations.get(documentKey)?.find(a => a.id === updatedAnnotation.id), // Preserve any fields not included in the update
             document: updatedAnnotation.document || currentDocumentText // Ensure the annotation's document field is updated to match the current document text
           } 
         : a

From edd9b56c7bb3607a60619fc97c74811d0f1dd780 Mon Sep 17 00:00:00 2001
From: Edward Misback <misback@cs.washington.edu>
Date: Wed, 8 Apr 2026 20:38:19 -0400
Subject: [PATCH 12/22] small fixes for demo

---
 .../webview-ui/src/additionalTools.tsx        |  2 +-
 vscode-extension/webview-ui/src/tools.tsx     | 28 ++++++++++---------
 2 files changed, 16 insertions(+), 14 deletions(-)

diff --git a/vscode-extension/webview-ui/src/additionalTools.tsx b/vscode-extension/webview-ui/src/additionalTools.tsx
index 893798e..641d785 100644
--- a/vscode-extension/webview-ui/src/additionalTools.tsx
+++ b/vscode-extension/webview-ui/src/additionalTools.tsx
@@ -1909,7 +1909,7 @@ REQUIREMENTS:
 2. Do NOT include: imports, export statements, or the component function declaration
 3. Use React hooks (useState, useEffect, useRef) as needed - they're available from React destructuring
 4. Store all state in metadata using props.utils.setMetadata() for persistence
-5. Use the commonTextStyle constant for consistent styling: { fontFamily: "Poppins, sans-serif", fontSize: "14px", color: "black" }
+5. Use the commonTextStyle constant for consistent styling: { fontFamily: "Poppins, sans-serif", fontSize: "14px", color: "black" }, but do not declare it, it is global.
 6. Include comprehensive console.log statements for debugging with format: console.log('[ComponentName] message', data)
 7. Handle errors gracefully with try-catch blocks
 8. The lmApi is available with this EXACT signature:
diff --git a/vscode-extension/webview-ui/src/tools.tsx b/vscode-extension/webview-ui/src/tools.tsx
index f9c09bb..d02cbfe 100644
--- a/vscode-extension/webview-ui/src/tools.tsx
+++ b/vscode-extension/webview-ui/src/tools.tsx
@@ -339,35 +339,37 @@ const Odyssey: React.FC<AnnotationEditorProps> = (props) => {
 
 /* TODO: Add all tools to be used here. */
 export const tools = {
+  MarkdownNote: MarkdownNote,
+  debugExample: ShowDebuggedExample,
+  yesNoQuestion: LMUnitTest,
+  odyssey: Odyssey,
+  Generator: Generator,
   comment: Comment,
   colorPicker: ColorPicker,
   // runCodeSegment: RunCodeSegment,
   imageUpload: ImageUpload,
   displayHTML: DisplayHTML,
-  odyssey: Odyssey,
-  yesNoQuestion: LMUnitTest,
-  debugExample: ShowDebuggedExample,
   explainInEnglish: ExplainInEnglish,
-  outputVisualizer: OutputVisualizer,
-  formalSpecification: FormalSpecification,
-  Generator: Generator,
-  MarkdownNote: MarkdownNote,
+  // outputVisualizer: OutputVisualizer,
+  // formalSpecification: FormalSpecification,
   // lmApiTest: LMAPITest,
 };
 
 export const toolNames = {
+  MarkdownNote: "Markdown Note",
+  Generator: "Annotation Generator",
+  yesNoQuestion: "LM Unit Test",
+  odyssey: "Analyze Floating-point Expression",
   comment: "Comment",
   colorPicker: "Color Picker",
   // runCodeSegment: "Run Code Segment",
   imageUpload: "Image Upload",
   displayHTML: "HTML Preview",
-  odyssey: "Analyze Floating-point Expression",
-  yesNoQuestion: "LM Unit Test",
   debugExample: "Show an Example",
   explainInEnglish: "Explain in English",
-  outputVisualizer: "Output Visualizer",
-  formalSpecification: "Formal Specification",
-  Generator: "Annotation Generator",
-  MarkdownNote: "Markdown Note",
+  // outputVisualizer: "Output Visualizer",
+  // formalSpecification: "Formal Specification",
+  
+  
   // lmApiTest: "LM API Test",
 };

From f5a615ecb7a1e1efb2cb2347b1dd3e2ad739da10 Mon Sep 17 00:00:00 2001
From: Edward Misback <misback@cs.washington.edu>
Date: Wed, 8 Apr 2026 20:38:40 -0400
Subject: [PATCH 13/22] bump version

---
 vscode-extension/package.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/vscode-extension/package.json b/vscode-extension/package.json
index 0c7079a..ac07a51 100644
--- a/vscode-extension/package.json
+++ b/vscode-extension/package.json
@@ -4,7 +4,7 @@
   "publisher": "codetations",
   "repository": "github:elmisback/codetations",
   "description": "Rich code annotations for VS Code",
-  "version": "0.0.27",
+  "version": "0.0.28",
   "engines": {
     "vscode": "^1.110.0"
   },

From f85aacf75c4e8230e2486f8a217f7b35871e1da4 Mon Sep 17 00:00:00 2001
From: Edward Misback <misback@cs.washington.edu>
Date: Fri, 10 Apr 2026 00:05:07 -0400
Subject: [PATCH 14/22] Misc patches for the video

---
 vscode-extension/src/AnnotationTracker.ts           | 1 +
 vscode-extension/webview-ui/src/App.tsx             | 9 ++++++++-
 vscode-extension/webview-ui/src/additionalTools.tsx | 2 +-
 3 files changed, 10 insertions(+), 2 deletions(-)

diff --git a/vscode-extension/src/AnnotationTracker.ts b/vscode-extension/src/AnnotationTracker.ts
index 4e39354..2733839 100644
--- a/vscode-extension/src/AnnotationTracker.ts
+++ b/vscode-extension/src/AnnotationTracker.ts
@@ -702,6 +702,7 @@ export class AnnotationTracker implements vscode.Disposable {
       });
       console.debug("finished updating document text to match annotation for", updatedAnnotation);
       const updatedDoc = await vscode.workspace.openTextDocument(document.uri);
+      await this.saveAnnotationsForDocument(updatedDoc);
       await this.updateDecorations(updatedDoc);
       return; // Wait for the document update to trigger the annotation update through the change listener
       // NOTE I didn't think hard about this, it might not work as expected for unusual updates.
diff --git a/vscode-extension/webview-ui/src/App.tsx b/vscode-extension/webview-ui/src/App.tsx
index 320a917..cc801fe 100644
--- a/vscode-extension/webview-ui/src/App.tsx
+++ b/vscode-extension/webview-ui/src/App.tsx
@@ -5,6 +5,7 @@ import { tools, toolNames } from "./tools";
 import React, { useState, useEffect, useRef } from "react";
 
 interface AnnotationUpdate {
+  end?: number;
   document?: string;
   metadata?: any;
 }
@@ -44,6 +45,7 @@ function AnnotationEditorContainer(props: {
           getText: () => value.document.slice(value.start, value.end),
           setText: (newText: string) => {
             setValue({
+              end: value.start + newText.length,
               document:
                 value.document.slice(0, value.start) + newText + value.document.slice(value.end),
               metadata: value.metadata,
@@ -155,6 +157,7 @@ function AnnotationSidebarView(props: {
     
     const updatedAnnotation = {
       ...annotation,
+      ...value,
       ...(value.document ? { document: value.document } : {document: undefined}),
       ...(value.metadata ? { metadata: { ...annotation.metadata, ...value.metadata } } : {})
     };
@@ -259,15 +262,19 @@ function RetagBanner(props: {
 }) {
   return (
     <div className="retag-banner" style={{ 
+      position: 'sticky',
+      top: 0,
+      zIndex: 1000,
       padding: "10px", 
       marginBottom: "10px", 
       backgroundColor: "#ffe0e0", 
       borderRadius: "4px",
+      boxShadow: '0 2px 8px rgba(0,0,0,0.12)',
       display: "flex",
       justifyContent: "space-between",
       alignItems: "center"
     }}>
-      <span>Document has been edited and some annotations need updating</span>
+      <span>Document has been edited and some annotations need updating</span>&nbsp;
       <div>
         <button onClick={props.onRetag} style={{ marginRight: "8px" }}>Update Annotations</button>
       </div>
diff --git a/vscode-extension/webview-ui/src/additionalTools.tsx b/vscode-extension/webview-ui/src/additionalTools.tsx
index 641d785..c6ca4ae 100644
--- a/vscode-extension/webview-ui/src/additionalTools.tsx
+++ b/vscode-extension/webview-ui/src/additionalTools.tsx
@@ -1913,7 +1913,7 @@ REQUIREMENTS:
 6. Include comprehensive console.log statements for debugging with format: console.log('[ComponentName] message', data)
 7. Handle errors gracefully with try-catch blocks
 8. The lmApi is available with this EXACT signature:
-   const response = await lmApi.chat(messages, { vendor: 'copilot', family: 'gpt-4o', temperature: 0.32 });
+   const response = await lmApi.chat(messages, { vendor: 'copilot', family: 'gpt-5.4-mini', temperature: 0.32 });
    IMPORTANT: lmApi.chat() returns a STRING directly, NOT an object. Use it like: const text = await lmApi.chat(messages, options);
 9. Use props.value.document to understand code context for better defaults and behavior
 10. Keep explanations and messages concise and user-friendly

From 99afa08417dd7769ffe611a9247b96cf28594d3b Mon Sep 17 00:00:00 2001
From: Edward Misback <misback@cs.washington.edu>
Date: Fri, 10 Apr 2026 00:05:26 -0400
Subject: [PATCH 15/22] Major retagging fix.

---
 vscode-extension/src/server/retag.ts | 49 +++++++++++++++++++++-------
 1 file changed, 38 insertions(+), 11 deletions(-)

diff --git a/vscode-extension/src/server/retag.ts b/vscode-extension/src/server/retag.ts
index 0f8d455..2a35b95 100644
--- a/vscode-extension/src/server/retag.ts
+++ b/vscode-extension/src/server/retag.ts
@@ -97,15 +97,15 @@ You are responsible for placing an identical annotation on this updated file. It
 
 Describe possible sections the specific segment could be said to be located in. It is possible the segment has not changed, or that it has been refactored. Pick the most correct choice. Remember to be detailed about the start and stop of the segment. If the segment has been updated, it may need to expand or shrink. BE CAREFUL TO INCLUDE NOTHING EXTRA. Then, provide the following numbered answers as a JSON object:
 
-1) Print ONLY the text of the updated specific segment. You must print all of the text here.
+1-code) Print ONLY the text of the updated specific segment. You must print all of the text here.
 
-2) State ONLY the line number in UPDATED that (1) starts on.
+2-start) State ONLY the line number in UPDATED that (1) starts on.
 
-3) State ONLY the line number in UPDATED that (1) ends on.
+3-end) State ONLY the line number in UPDATED that (1) ends on.
 
-4) (1) may occur multiple times in the section given by [(2),(3)]. Which number occurrence, as ONLY a 1-indexed number, is (1)?
+4-occurrence) (1) may occur multiple times in the section given by [(2),(3)]. Which number occurrence, as ONLY a 1-indexed number, is (1)?
 
-The object must look like: {1: <code>, 2: <number>, 3: <number>, 4: <number>}
+The object must look like: {"code": "<code>", "start": <number>, "end": <number>, "occurrence": <number>}
 
 The answer to 1 should be a code string only, without markdown formatting or extra notes.`;
 
@@ -204,7 +204,8 @@ const retagUpdate = async (
       codeWithSnippetDelimited,
       updatedCodeWithSnippetDelimited: updatedCodeWithoutDelimiters,
       delimiter,
-    }) ) || '';
+    })) || '';
+    console.log("Raw output from model:", gptOut);
     console.log(gptOut);
   } catch (e) {
     return { error: e, errorType: "model" };
@@ -212,7 +213,7 @@ const retagUpdate = async (
   let gptRetaggingJSON;
   try {
     gptRetaggingJSON = JSON.parse(gptOut);
-    console.log(gptRetaggingJSON);
+    console.log("gptRetaggingJSON:", gptRetaggingJSON);
   } catch (e) {
     // (This should never happen based on the OpenAI documentation.)
     return { error: e, errorType: "JSON parse", gptOut };
@@ -246,6 +247,7 @@ const retagUpdate = async (
     delimiterStart: string;
     delimiterEnd: string;
   };
+  console.log("Parsed JSON from model:", gptRetaggingJSON);
 
   const computeUpdatedCodeWithSnippetRetagged = ({
     code,
@@ -265,6 +267,31 @@ const retagUpdate = async (
         would guarantee placement in the "intended" location,
         but this is slow
     */
+    // first check for the simple case where we can just split the file on the index of the starting line, find the snippet in that section, and then add the delimiters based on the index of the snippet in that section.
+    
+    // console.log("Attempting to find snippet in identified lines", { lineStart, lineEnd, snippet });
+    // const splitIdx = code
+    //   .split("\n")
+    //   .slice(0, lineStart)
+    //   .map((s) => s + "\n")
+    //   .join("").length;
+    
+    // const findIdx = code.slice(splitIdx).indexOf(snippet);
+    // console.log("Find indices:", { splitIdx, findIdx });
+    // if (findIdx !== -1) {
+    //   const leftIdx = splitIdx + findIdx;
+    //   const rightIdx = leftIdx + snippet.length;
+    //   return {
+    //     updatedCodeWithDelimiters:
+    //       code.slice(0, leftIdx) +
+    //       delimiterStart +
+    //       code.slice(leftIdx, rightIdx) +
+    //       delimiterEnd +
+    //       code.slice(rightIdx, code.length),
+    //     leftIdx,
+    //     rightIdx,
+    //   };
+    // }
 
     let sectionString = code
       .split("\n")
@@ -309,10 +336,10 @@ const retagUpdate = async (
   try {
     const out = computeUpdatedCodeWithSnippetRetagged({
       code: updatedCodeWithoutDelimiters,
-      snippet: gptRetaggingJSON[1],
-      lineStart: gptRetaggingJSON[2],
-      lineEnd: gptRetaggingJSON[3],
-      nthOccurrence: gptRetaggingJSON[4],
+      snippet: gptRetaggingJSON.code,
+      lineStart: gptRetaggingJSON.start,
+      lineEnd: gptRetaggingJSON.end,
+      nthOccurrence: gptRetaggingJSON.occurrence,
       delimiterStart: delimiter,
       delimiterEnd: delimiter,
     });

From ec19b1682acdf3f5df905744e5c51ede9348d9d8 Mon Sep 17 00:00:00 2001
From: Edward Misback <misback@cs.washington.edu>
Date: Tue, 14 Apr 2026 23:10:37 -0400
Subject: [PATCH 16/22] Refactor as testable functional code.

---
 vscode-extension/src/AnnotationTracker.ts | 1326 ++++++++++-----------
 vscode-extension/src/extension.ts         |    6 +-
 2 files changed, 630 insertions(+), 702 deletions(-)

diff --git a/vscode-extension/src/AnnotationTracker.ts b/vscode-extension/src/AnnotationTracker.ts
index 2733839..fe4c83c 100644
--- a/vscode-extension/src/AnnotationTracker.ts
+++ b/vscode-extension/src/AnnotationTracker.ts
@@ -3,6 +3,7 @@ import * as path from "path";
 import * as fs from "fs";
 import { createPatch, applyPatch } from "diff";
 import { AnnotationManagerPanel } from "./panels/AnnotationManagerPanel";
+
 export interface Annotation {
   // HACK this just duplicates "../webview-ui/src/Annotation.tsx"
   id: string;
@@ -20,758 +21,685 @@ export interface Annotation {
   };
 }
 
-interface AnnotationState {
-  annotations: Annotation[];
+export interface TrackerState {
+  documentAnnotations: Map<string, Annotation[]>;
+  decorationTypes: Map<string, vscode.TextEditorDecorationType[]>;
+  fileChangeTimers: Map<string, NodeJS.Timeout>;
+  documentContentCache: Map<string, string>;
+  pendingChanges: Map<string, vscode.TextDocumentContentChangeEvent[]>;
 }
 
-export class AnnotationTracker implements vscode.Disposable {
-  private disposables: vscode.Disposable[] = [];
-  private documentAnnotations: Map<string, Annotation[]> = new Map();
-  private decorationTypes: Map<string, vscode.TextEditorDecorationType[]> = new Map();
-  private fileChangeTimers: Map<string, NodeJS.Timeout> = new Map();
-  
-  // Store the document content cache
-  private documentContentCache = new Map<string, string>();
-  
-  // Track accumulated changes for proper position updates
-  private pendingChanges = new Map<string, vscode.TextDocumentContentChangeEvent[]>();
-  
-  constructor(private context: vscode.ExtensionContext) {
-    // Setup buffer change listeners
-    this.disposables.push(
-      vscode.workspace.onDidChangeTextDocument(this.onDocumentChanged, this),
-      vscode.window.onDidChangeActiveTextEditor(this.onActiveEditorChanged, this)
-    );
-    
-    // Load initial annotations if there's an active editor
-    if (vscode.window.activeTextEditor) {
-      this.loadAnnotationsForDocument(vscode.window.activeTextEditor.document);
+
+// ═══════════════════════════════════════════════════════════════════════════════
+// Pure functions — exported for testing. These never touch TrackerState.
+// ═══════════════════════════════════════════════════════════════════════════════
+
+export function getAnnotationsFilePath(documentPath: string, createDir: boolean = false): string {
+  let currentDir = path.dirname(documentPath);
+
+  while (currentDir !== path.parse(currentDir).root) {
+    if (fs.existsSync(path.join(currentDir, ".git"))) {
+      break;
     }
+    currentDir = path.dirname(currentDir);
   }
 
-  /**
-   * Loads annotations for the given document from the associated annotations file
-   */
-  public async loadAnnotationsForDocument(document: vscode.TextDocument): Promise<Annotation[]> {
-    const documentKey = document.uri.toString();
-    const annotationsUri = this.getAnnotationsFilePath(document.uri.fsPath);
-    console.debug(`Loading annotations for ${documentKey} from ${annotationsUri}`);
-    // TODO we have only sort-of validated that diff loading works correctly.
-    if (this.documentAnnotations.has(documentKey)) {
-      // Already loaded
-      return this.documentAnnotations.get(documentKey) as Annotation[];
-    }
-    try {
-      // Check if file exists
-      if (fs.existsSync(annotationsUri)) {
-        const content = fs.readFileSync(annotationsUri, "utf8");
-        const state = JSON.parse(content) as { document: string; annotations: (Annotation & { documentDiff?: string })[] };
-        
-        // Reconstruct each annotation's document field using applyPatch
-        const reconstructedAnnotations = state.annotations.map(ann => {
-          const reconstructedDoc = 
-            ann.documentDiff ?
-              applyPatch(state.document, ann.documentDiff) || state.document
-            : ann.document || state.document;
-          const originalDoc =
-            ann.original.documentDiff ?
-              applyPatch(state.document, ann.original.documentDiff) || reconstructedDoc
-            : ann.original.document;
-          return {
-            ...ann,
-            document: reconstructedDoc,
-            original: {
-              ...ann.original,
-              document: originalDoc
-            }
-          };
-        });
-        
-        // Store annotations for this document
-        this.documentAnnotations.set(documentKey, reconstructedAnnotations as Annotation[]);
-        
-        // Update decorations
-        this.updateDecorations(document);
-        
-        // Notify the webview if it's open
-        this.notifyAnnotationsChanged(document);
-        
-        return reconstructedAnnotations as Annotation[];
-      } else {
-        // No annotations file yet
-        this.documentAnnotations.set(documentKey, []);
-        return [];
-      }
-    } catch (error) {
-      console.error(`Error loading annotations for ${documentKey}:`, error);
-      this.documentAnnotations.set(documentKey, []);
-      return [];
-    }
+  const relPath = path.relative(currentDir, documentPath);
+  const annotationsDir = path.join(currentDir, "codetations", path.dirname(relPath));
+
+  if (createDir && !fs.existsSync(annotationsDir)) {
+    fs.mkdirSync(annotationsDir, { recursive: true });
   }
 
-  /**
-   * Saves annotations for the given document to the associated annotations file
-   */
-  public async saveAnnotationsForDocument(document: vscode.TextDocument): Promise<void> {
-    const documentKey = document.uri.toString();
-    const annotations = this.documentAnnotations.get(documentKey) || [];
-    
-    // Only save if there are annotations
-    if (annotations.length === 0) {
-      return;
+  return path.join(annotationsDir, path.basename(documentPath) + ".annotations.json");
+}
+
+export function reconstructAnnotationsFromDisk(diskState: {
+  document: string;
+  annotations: (Annotation & { documentDiff?: string })[];
+}): Annotation[] {
+  return diskState.annotations.map((ann) => {
+    const reconstructedDoc = ann.documentDiff
+      ? applyPatch(diskState.document, ann.documentDiff) || diskState.document
+      : ann.document || diskState.document;
+
+    const originalDoc = ann.original.documentDiff
+      ? applyPatch(diskState.document, ann.original.documentDiff) || reconstructedDoc
+      : ann.original.document;
+
+    return {
+      ...ann,
+      document: reconstructedDoc,
+      original: { ...ann.original, document: originalDoc },
+    };
+  });
+}
+
+export function serializeAnnotationsForDisk(
+  annotations: Annotation[],
+  documentText: string,
+  fileName: string
+): { document: string; annotations: object[] } {
+  const globalDocument = annotations.length > 0 ? annotations[0].document : documentText;
+
+  const serialized = annotations.map((ann) => {
+    const { document: annDoc, ...rest } = ann;
+
+    let documentDiff: string | undefined;
+    if (annDoc !== globalDocument) {
+      try {
+        documentDiff = createPatch(fileName, globalDocument, annDoc);
+      } catch (e) {
+        documentDiff = undefined;
+        console.error("Error creating document diff:", e);
+      }
     }
-    
-    const annotationsUri = this.getAnnotationsFilePath(document.uri.fsPath, true);
 
-    // Ensure directory exists
-    const dir = path.dirname(annotationsUri);
-    if (!fs.existsSync(dir)) {
-      fs.mkdirSync(dir, { recursive: true });
+    const {
+      original: { document: originalDocument, ...restOriginal },
+    } = ann;
+
+    let originalDocumentDiff: string | undefined;
+    if (originalDocument !== globalDocument) {
+      try {
+        originalDocumentDiff = createPatch(fileName, globalDocument, originalDocument);
+      } catch (e) {
+        originalDocumentDiff = undefined;
+        console.error("Error creating original document diff:", e);
+      }
     }
-    console.debug(`Saving annotations for ${documentKey} to ${annotationsUri}`);
-
-    // Save the global document string
-    const globalDocument = annotations.length > 0 ? annotations[0].document : document.getText();
-
-    // Write annotations to file with documentDiffs
-    const state = {
-      document: globalDocument,
-      annotations: annotations.map(ann => {
-        // Remove local document field, replace with documentDiff
-        const { document: annDoc, ...rest } = ann;
-        // Compute diff from global document to annotation's document
-        let documentDiff = undefined;
-        if (annDoc !== globalDocument) {
-          try {
-            documentDiff = createPatch(document.fileName, globalDocument, annDoc);
-          } catch (e) {
-            documentDiff = undefined;
-            console.error("Error creating document diff:", e);
-          }
-        }
-        const { original: {
-          document: originalDocument,
-          ...restOriginal
-        } } = ann;
-        let originalDocumentDiff = undefined;
-        if (originalDocument !== globalDocument) {
-          try {
-            originalDocumentDiff = createPatch(document.fileName, globalDocument, originalDocument);
-          } catch (e) {
-            originalDocumentDiff = undefined;
-            console.error("Error creating original document diff:", e);
-          }
-        }
-        return {
-          ...rest,
-          documentDiff,
-          original: {
-            ...restOriginal,
-            documentDiff: originalDocumentDiff
-          }
-        };
-      })
+
+    return {
+      ...rest,
+      documentDiff,
+      original: { ...restOriginal, documentDiff: originalDocumentDiff },
     };
-    fs.writeFileSync(annotationsUri, JSON.stringify(state, null, 2), "utf8");
+  });
+
+  return { document: globalDocument, annotations: serialized };
+}
+
+export function applyChangesToAnnotations(
+  annotations: Annotation[],
+  changes: readonly vscode.TextDocumentContentChangeEvent[],
+  startingContent: string,
+  currentContent: string
+): Annotation[] {
+  if (startingContent === currentContent) {
+    return annotations;
   }
 
-  /**
-   * Handler for document changes - collects changes for batch processing
-   */
-  private onDocumentChanged(event: vscode.TextDocumentChangeEvent): void {
-    // Skip if document is not loaded
-    if (!this.documentAnnotations.has(event.document.uri.toString())) {
-      return;
-    }
+  let current = annotations;
 
-    const docKey = event.document.uri.toString();
-    
-    // Initialize document content cache if not already set
-    if (!this.documentContentCache.has(docKey)) {
-      this.documentContentCache.set(docKey, event.document.getText());
-      return;
-    }
-    
-    // Collect changes for this document
-    let pendingChanges = this.pendingChanges.get(docKey) || [];
-    pendingChanges = [...pendingChanges, ...event.contentChanges];
-    this.pendingChanges.set(docKey, pendingChanges);
-    
-    // Debounce the processing of changes
-    if (this.fileChangeTimers.has(docKey)) {
-      clearTimeout(this.fileChangeTimers.get(docKey)!);
-    }
+  for (const change of changes) {
+    const startOffset = change.rangeOffset;
+    const endOffset = change.rangeOffset + change.rangeLength;
+    const textLengthDiff = change.text.length - change.rangeLength;
+    const isWhitespaceChange = /^\s*$/.test(change.text);
 
-    this.fileChangeTimers.set(docKey, setTimeout(() => {
-      const editor = vscode.window.activeTextEditor;
-      if (!editor || editor.document.uri.toString() !== docKey) {
-        console.error("Editor not active or document not loaded", editor, editor?.document.uri.toString(), docKey);
-        this.pendingChanges.delete(docKey);
-        this.fileChangeTimers.delete(docKey);
-        return;
+    current = current.map((annotation) => {
+      if (annotation.document !== startingContent) {
+        return annotation;
       }
-      
-      // Process all accumulated changes at once
-      this.processAccumulatedChanges(editor.document);
-      
-      // Update cache and cleanup
-      this.documentContentCache.set(docKey, editor.document.getText());
-      this.pendingChanges.delete(docKey);
-      this.fileChangeTimers.delete(docKey);
-    }, 50));
-  }
 
-  /**
-   * Process all accumulated changes for a document
-   */
-  private processAccumulatedChanges(document: vscode.TextDocument): void {
-    const documentKey = document.uri.toString();
-    const annotations = this.documentAnnotations.get(documentKey);
-    const changes = this.pendingChanges.get(documentKey) || [];
-    
-    if (!annotations || annotations.length === 0 || changes.length === 0) {
-      return;
-    }
-    
-    // Get the cached document content before any changes
-    const startingContent = this.documentContentCache.get(documentKey)!;
-    const currentContent = document.getText();
-    
-    // Skip if no actual change occurred
-    if (startingContent === currentContent) {
-      return;
-    }
-    
-    // Create working copies of annotations that we can update
-    // These working copies will maintain their position references relative to startingContent
-    let workingAnnotations = annotations.map(ann => ({...ann}));
-    
-    // Apply each change one by one to compute the new positions
-    for (const change of changes) {
-      const startOffset = change.rangeOffset;
-      const endOffset = change.rangeOffset + change.rangeLength;
-      const textLengthDiff = change.text.length - change.rangeLength;
-      
-      // Check if the change is only whitespace
-      const isWhitespaceChange = /^\s*$/.test(change.text);
-      
-      for (let i = 0; i < workingAnnotations.length; i++) {
-        const annotation = workingAnnotations[i];
-        
-        // Skip annotations that don't match the current document content
-        if (annotation.document !== startingContent) {
-          continue;
-        }
-        
-        // CASE 1: Change is completely before the annotation
-        if (endOffset < annotation.start) {
-          // Simply shift the annotation
-          annotation.start += textLengthDiff;
-          annotation.end += textLengthDiff;
-          continue;
-        }
-        
-        // CASE 2: Change is completely after the annotation
-        if (startOffset > annotation.end) {
-          // No adjustment needed
-          continue;
-        }
-        
-        // CASE 3: Change is adjacent to the annotation (immediately before)
-        if (endOffset === annotation.start) {
-          // If not whitespace, include it in the annotation
-          if (!isWhitespaceChange) {
-            annotation.start = startOffset;
-            annotation.end += textLengthDiff;
-          } else {
-            // If whitespace, just shift the annotation
-            annotation.start += textLengthDiff;
-            annotation.end += textLengthDiff;
-          }
-          continue;
-        }
-        
-        // CASE 4: Change is adjacent to the annotation (immediately after)
-        if (startOffset === annotation.end) {
-          // If not whitespace, include it in the annotation
-          if (!isWhitespaceChange) {
-            annotation.end += change.text.length;
-          }
-          // If whitespace, don't expand the annotation
-          continue;
-        }
-        
-        // CASE 5: Change is completely inside the annotation
-        if (startOffset >= annotation.start && endOffset <= annotation.end) {
-          // Grow or shrink the annotation by the exact amount of the change
-          annotation.end += textLengthDiff;
-          continue;
-        }
-        
-        // CASE 6: Change partially overlaps with the start of the annotation
-        if (startOffset < annotation.start && endOffset > annotation.start && endOffset <= annotation.end) {
-          // If the change contains whitespace at the beginning or end, determine how to handle
-          if (isWhitespaceChange) {
-            // For whitespace changes, adjust start to after the whitespace
-            annotation.start = startOffset + change.text.length;
-            annotation.end += textLengthDiff;
-          } else {
-            // For non-whitespace changes, include the change
-            annotation.start = startOffset;
-            annotation.end += textLengthDiff;
-          }
-          continue;
-        }
-        
-        // CASE 7: Change partially overlaps with the end of the annotation
-        if (startOffset >= annotation.start && startOffset < annotation.end && endOffset > annotation.end) {
-          // If the change contains whitespace at the beginning or end, determine how to handle
-          if (isWhitespaceChange) {
-            // For whitespace changes, don't expand the annotation
-            annotation.end = startOffset;
-          } else {
-            // For non-whitespace changes, include the change
-            annotation.end = startOffset + change.text.length;
-          }
-          continue;
+      // CASE 1: Change is completely before the annotation
+      if (endOffset < annotation.start) {
+        return { ...annotation, start: annotation.start + textLengthDiff, end: annotation.end + textLengthDiff };
+      }
+
+      // CASE 2: Change is completely after the annotation
+      if (startOffset > annotation.end) {
+        return annotation;
+      }
+
+      // CASE 3: Change is adjacent to the annotation (immediately before)
+      if (endOffset === annotation.start) {
+        if (!isWhitespaceChange) {
+          return { ...annotation, start: startOffset, end: annotation.end + textLengthDiff };
         }
-        
-        // CASE 8: Change completely contains the annotation
-        if (startOffset < annotation.start && endOffset > annotation.end) {
-          if (change.text.length === 0) {
-            // If the text is deleted, collapse the annotation
-            annotation.start = startOffset;
-            annotation.end = startOffset;
-          } else if (isWhitespaceChange) {
-            // If change is whitespace, try to maintain relative position
-            annotation.start = startOffset;
-            annotation.end = startOffset;
-          } else {
-            // Otherwise, try to map to some portion of the new text
-            annotation.start = startOffset;
-            annotation.end = startOffset + change.text.length;
-          }
-          continue;
+        return { ...annotation, start: annotation.start + textLengthDiff, end: annotation.end + textLengthDiff };
+      }
+
+      // CASE 4: Change is adjacent to the annotation (immediately after)
+      if (startOffset === annotation.end) {
+        if (!isWhitespaceChange) {
+          return { ...annotation, end: annotation.end + change.text.length };
         }
+        return annotation;
       }
-    }
-    
-    // Update all annotations with the current document content
-    const finalAnnotations = workingAnnotations.map(ann => ({
-      ...ann,
-      document: ann.document !== startingContent ? ann.document : currentContent
-    }));
-    
-    // Update the document's annotations
-    this.documentAnnotations.set(documentKey, finalAnnotations);
-    
-    // Update decorations, save, and notify
-    this.updateDecorations(document);
-    this.saveAnnotationsForDocument(document);
-    this.notifyAnnotationsChanged(document);
-  }
 
-  /**
-   * Updates the decorations in the editor
-   */
-  public updateDecorations(document: vscode.TextDocument): void {
-    console.log("Updating decorations for document", document.uri.toString());
-    const documentKey = document.uri.toString();
-    console.log(this.documentAnnotations.get(documentKey));
-    const annotations = this.documentAnnotations.get(documentKey) || [];
-    
-    // Clear existing decorations
-    this.clearDecorations(documentKey);
-    
-    // Find editors displaying this document
-    const editors = vscode.window.visibleTextEditors.filter(
-      editor => editor.document.uri.toString() === documentKey
-    );
-    
-    if (editors.length === 0) {
-      return; // No visible editor for this document
-    }
-    
-    // Get selected annotation ID from the panel if available
-    const selectedAnnotationId = AnnotationManagerPanel.currentPanel?.selectedAnnotationId;
-    
-    const decorations: vscode.TextEditorDecorationType[] = [];
-    
-    // Create and apply decorations for each annotation
-    for (const annotation of annotations) {
-      // Skip if the document text doesn't match the annotation's document
-      if (annotation.document !== document.getText()) {
-        continue;
+      // CASE 5: Change is completely inside the annotation
+      if (startOffset >= annotation.start && endOffset <= annotation.end) {
+        return { ...annotation, end: annotation.end + textLengthDiff };
       }
-      try {
-        // Check if this is the selected annotation
-        const isSelected = selectedAnnotationId === annotation.id;
-        
-        // Extract base color from metadata or use default
-        const baseColor = annotation.metadata?.color || "rgba(255,255,0,0.3)";
-        
-        // Increase opacity for selected annotation
-        let decorationColor = baseColor;
-        if (isSelected) {
-          if (baseColor.startsWith("rgba")) {
-            // Parse the rgba color values
-            const rgbaMatch = baseColor.match(/rgba\((\d+),\s*(\d+),\s*(\d+),\s*([\d.]+)\)/);
-            if (rgbaMatch) {
-              const [_, r, g, b] = rgbaMatch;
-              // Use a fixed higher opacity value for selected annotations
-              decorationColor = `rgba(${r}, ${g}, ${b}, 0.5)`;
-            }
-          } else if (baseColor.startsWith("rgb")) {
-            // For rgb format, add alpha
-            const rgbMatch = baseColor.match(/rgb\((\d+),\s*(\d+),\s*(\d+)\)/);            
-            if (rgbMatch) {
-              const [_, r, g, b] = rgbMatch;
-              decorationColor = `rgba(${r}, ${g}, ${b}, 0.5)`;
-            }
-          } else if (baseColor.startsWith("#")) {
-            // For hex format, convert to rgba
-            const hex = baseColor.slice(1);            
-            const r = parseInt(hex.substring(0, 2), 16);
-            const g = parseInt(hex.substring(2, 4), 16);
-            const b = parseInt(hex.substring(4, 6), 16);
-            decorationColor = `rgba(${r}, ${g}, ${b}, 0.5)`;
-          }
+
+      // CASE 6: Change partially overlaps with the start of the annotation
+      if (startOffset < annotation.start && endOffset > annotation.start && endOffset <= annotation.end) {
+        if (isWhitespaceChange) {
+          return { ...annotation, start: startOffset + change.text.length, end: annotation.end + textLengthDiff };
         }
-        
-        // Extract solid color for gutter without transparency
-        let gutterColor = baseColor;
-        if (gutterColor.startsWith("rgba")) {
-          // Convert rgba to rgb for the gutter
-          const rgbaMatch = baseColor.match(/rgba\((\d+),\s*(\d+),\s*(\d+),\s*([\d.]+)\)/);
-          if (rgbaMatch) {
-            const [_, r, g, b] = rgbaMatch;
-            gutterColor = `rgb(${r}, ${g}, ${b})`;
-          }
-        } else if (baseColor.startsWith("#")) {
-          // Keep hex color as is for gutter
-          gutterColor = baseColor;
+        return { ...annotation, start: startOffset, end: annotation.end + textLengthDiff };
+      }
+
+      // CASE 7: Change partially overlaps with the end of the annotation
+      if (startOffset >= annotation.start && startOffset < annotation.end && endOffset > annotation.end) {
+        if (isWhitespaceChange) {
+          return { ...annotation, end: startOffset };
         }
-        
-        // Create the decoration range
-        const startPos = document.positionAt(annotation.start);
-        const endPos = document.positionAt(annotation.end);
-        const range = new vscode.Range(startPos, endPos);
-        
-        // 1. Create text decoration type with highlighting and potential underline
-        const textDecorationType = vscode.window.createTextEditorDecorationType({
-          // backgroundColor: decorationColor,
-          borderColor: decorationColor,
-          borderStyle: true ? 'none none solid none' : 'none',
-          // Add underline for selected annotations
-          // textDecoration: isSelected ? 'underline' : undefined,
-          
-          // Add entries to the overview ruler
-          // overviewRulerColor: gutterColor,
-          // overviewRulerLane: vscode.OverviewRulerLane.Left
-        });
-        
-        // 2. Create gutter decoration type with vertical line
-        const gutterDecorationType = vscode.window.createTextEditorDecorationType({
-          isWholeLine: true,
-          // Left margin decoration - the vertical line
-          borderColor: gutterColor,
-          borderWidth: '3px',
-          borderStyle: 'none solid none none'
-        });
-        
-        // Apply both decorations to all editors
-        for (const editor of editors) {
-          editor.setDecorations(textDecorationType, [range]);
-          editor.setDecorations(gutterDecorationType, [range]);
+        return { ...annotation, end: startOffset + change.text.length };
+      }
+
+      // CASE 8: Change completely contains the annotation
+      if (startOffset < annotation.start && endOffset > annotation.end) {
+        if (change.text.length === 0 || isWhitespaceChange) {
+          return { ...annotation, start: startOffset, end: startOffset };
         }
-        
-        // Store both decoration types
-        decorations.push(textDecorationType);
-        decorations.push(gutterDecorationType);
-        
-      } catch (error) {
-        console.error("Error creating decoration:", error);
+        return { ...annotation, start: startOffset, end: startOffset + change.text.length };
       }
-    }
-    
-    // Store the new decoration types
-    this.decorationTypes.set(documentKey, decorations);
+
+      return annotation;
+    });
   }
 
-  /**
-   * Clears decorations for a document
-   */
-  private clearDecorations(documentKey: string): void {
-    const types = this.decorationTypes.get(documentKey);
-    if (!types) {return;}
-    
-    for (const type of types) {
-      type.dispose();
-    }
-    
-    this.decorationTypes.set(documentKey, []);
+  return current.map((ann) =>
+    ann.document === startingContent ? { ...ann, document: currentContent } : ann
+  );
+}
+
+export function resolveDecorationColor(baseColor: string, isSelected: boolean): string {
+  if (!isSelected) {
+    return baseColor;
+  }
+  if (baseColor.startsWith("rgba")) {
+    const m = baseColor.match(/rgba\((\d+),\s*(\d+),\s*(\d+),\s*([\d.]+)\)/);
+    if (m) { return `rgba(${m[1]}, ${m[2]}, ${m[3]}, 0.5)`; }
+  } else if (baseColor.startsWith("rgb")) {
+    const m = baseColor.match(/rgb\((\d+),\s*(\d+),\s*(\d+)\)/);
+    if (m) { return `rgba(${m[1]}, ${m[2]}, ${m[3]}, 0.5)`; }
+  } else if (baseColor.startsWith("#")) {
+    const hex = baseColor.slice(1);
+    const r = parseInt(hex.substring(0, 2), 16);
+    const g = parseInt(hex.substring(2, 4), 16);
+    const b = parseInt(hex.substring(4, 6), 16);
+    return `rgba(${r}, ${g}, ${b}, 0.5)`;
   }
+  return baseColor;
+}
 
-  /**
-   * Handler for active editor changes
-   */
-  private onActiveEditorChanged(editor: vscode.TextEditor | undefined): void {
-    if (!editor) {return;}
-    
-    // Load annotations for the new editor
-    this.loadAnnotationsForDocument(editor.document);
-    this.documentContentCache.set(editor.document.uri.toString(), editor.document.getText());
+export function resolveGutterColor(baseColor: string): string {
+  if (baseColor.startsWith("rgba")) {
+    const m = baseColor.match(/rgba\((\d+),\s*(\d+),\s*(\d+),\s*([\d.]+)\)/);
+    if (m) { return `rgb(${m[1]}, ${m[2]}, ${m[3]})`; }
   }
+  return baseColor;
+}
 
-  /**
-   * Notifies the annotation panel of changed annotations
-   */
-  private async notifyAnnotationsChanged(document: vscode.TextDocument): Promise<void> {
-    console.log("Notifying annotation panel of changes for document", document.uri.toString());
-    if (AnnotationManagerPanel.currentPanel) {
-      const documentKey = document.uri.toString();
-      const annotations = this.documentAnnotations.get(documentKey) || [];
-      
-      await AnnotationManagerPanel.currentPanel.sendMessageObject({
-        command: "updateAnnotations",
-        data: {
-          documentUri: document.uri.toString(),
-          annotations,
-          documentText: document.getText()
-        }
-      });
-    }
+export function annotationsAreIdentical(a: Annotation, b: Annotation): boolean {
+  return (
+    a.start === b.start &&
+    a.end === b.end &&
+    a.document === b.document &&
+    JSON.stringify(a.metadata) === JSON.stringify(b.metadata)
+  );
+}
+
+/**
+ * Returns a new annotations list with one annotation replaced by a patched version.
+ */
+export function patchAnnotationInList(
+  annotations: Annotation[],
+  annotationId: string,
+  patch: Partial<Annotation>,
+  fallbackDocument: string
+): Annotation[] {
+  return annotations.map((a) =>
+    a.id === annotationId
+      ? { ...a, ...patch, document: patch.document || fallbackDocument }
+      : a
+  );
+}
+
+
+// ═══════════════════════════════════════════════════════════════════════════════
+// I/O functions — read/write disk and VS Code APIs. No TrackerState access.
+// ═══════════════════════════════════════════════════════════════════════════════
+
+function readAnnotationsFromDisk(documentFsPath: string): Annotation[] | null {
+  const annotationsPath = getAnnotationsFilePath(documentFsPath);
+  console.debug(`Loading annotations from ${annotationsPath}`);
+
+  if (!fs.existsSync(annotationsPath)) {
+    return null;
   }
 
-  /**
-   * Gets the path to the annotations file for a document
-   */
-  private getAnnotationsFilePath(documentPath: string, createDir: boolean = false): string {
-    let currentDir = path.dirname(documentPath);
-    
-    // Look for git root or fall back to document directory
-    while (currentDir !== path.parse(currentDir).root) {
-      if (fs.existsSync(path.join(currentDir, ".git"))) {
-        break;
-      }
-      currentDir = path.dirname(currentDir);
-    }
-    
-    // Create the relative path for annotations
-    const relPath = path.relative(currentDir, documentPath);
-    const annotationsDir = path.join(currentDir, 'codetations', path.dirname(relPath));
-    
-    // Only ensure directory exists when createDir is true
-    // (Don't create directories when just building paths for reading)
-    if (createDir && !fs.existsSync(annotationsDir)) {
-      fs.mkdirSync(annotationsDir, { recursive: true });
+  try {
+    const content = fs.readFileSync(annotationsPath, "utf8");
+    const diskState = JSON.parse(content);
+    return reconstructAnnotationsFromDisk(diskState);
+  } catch (error) {
+    console.error(`Error loading annotations from ${annotationsPath}:`, error);
+    return null;
+  }
+}
+
+function writeAnnotationsToDisk(
+  annotations: Annotation[],
+  document: vscode.TextDocument
+): void {
+  if (annotations.length === 0) {
+    return;
+  }
+  const annotationsUri = getAnnotationsFilePath(document.uri.fsPath, true);
+  const dir = path.dirname(annotationsUri);
+  if (!fs.existsSync(dir)) {
+    fs.mkdirSync(dir, { recursive: true });
+  }
+  console.debug(`Saving annotations to ${annotationsUri}`);
+  const state = serializeAnnotationsForDisk(annotations, document.getText(), document.fileName);
+  fs.writeFileSync(annotationsUri, JSON.stringify(state, null, 2), "utf8");
+}
+
+function deleteAnnotationsFile(documentFsPath: string): void {
+  try {
+    const filePath = getAnnotationsFilePath(documentFsPath);
+    if (fs.existsSync(filePath)) {
+      fs.unlinkSync(filePath);
     }
-    
-    // Return full path to annotations file
-    return path.join(annotationsDir, path.basename(documentPath) + ".annotations.json");
+  } catch (error) {
+    console.error("Failed to remove annotations file:", error);
   }
+}
 
-  /**
-   * Adds a new annotation for the given document
-   */
-  public addAnnotation(document: vscode.TextDocument, annotation: Annotation): void {
-    const documentKey = document.uri.toString();
-    const annotations = this.documentAnnotations.get(documentKey) || [];
-    
-    // Add the new annotation
-    const updatedAnnotations = [...annotations, annotation];
-    this.documentAnnotations.set(documentKey, updatedAnnotations);
-    
-    // Update decorations and save
-    this.updateDecorations(document);
-    this.saveAnnotationsForDocument(document);
-    this.notifyAnnotationsChanged(document);
+function notifyPanel(document: vscode.TextDocument, annotations: Annotation[]): void {
+  console.log("Notifying annotation panel of changes for document", document.uri.toString());
+  if (AnnotationManagerPanel.currentPanel) {
+    AnnotationManagerPanel.currentPanel.sendMessageObject({
+      command: "updateAnnotations",
+      data: {
+        documentUri: document.uri.toString(),
+        annotations,
+        documentText: document.getText(),
+      },
+    });
   }
+}
 
-  /**
-   * Removes an annotation by ID
-   */
-  public removeAnnotation(document: vscode.TextDocument, annotationId: string): void {
-    const documentKey = document.uri.toString();
-    const annotations = this.documentAnnotations.get(documentKey) || [];
-    
-    // Filter out the annotation to remove
-    const updatedAnnotations = annotations.filter(a => a.id !== annotationId);
-    this.documentAnnotations.set(documentKey, updatedAnnotations);
-    
-    // Update decorations
-    this.updateDecorations(document);
-    
-    if (updatedAnnotations.length === 0) {
-      // If no annotations left, remove the file
-      try {
-        const annotationsFilePath = this.getAnnotationsFilePath(document.uri.fsPath);
-        if (fs.existsSync(annotationsFilePath)) {
-          fs.unlinkSync(annotationsFilePath);
-        }
-      } catch (error) {
-        console.error("Failed to remove annotations file:", error);
-      }
-    } else {
-      // Otherwise save updated annotations
-      this.saveAnnotationsForDocument(document);
+/**
+ * Disposes old decoration types for a document key, creates new ones from the
+ * given annotations, applies them to visible editors, and returns the new
+ * decoration type array.
+ */
+function rebuildDecorations(
+  oldDecorations: vscode.TextEditorDecorationType[] | undefined,
+  annotations: Annotation[],
+  document: vscode.TextDocument
+): vscode.TextEditorDecorationType[] {
+  const documentKey = document.uri.toString();
+
+  console.log("Updating decorations for document", documentKey);
+  console.log(annotations);
+
+  // Dispose old
+  if (oldDecorations) {
+    for (const d of oldDecorations) {
+      d.dispose();
     }
-    
-    // Notify the webview panel of the change
-    this.notifyAnnotationsChanged(document);
   }
 
-  /**
-   * Updates an existing annotation
-   * 
-   * forces changes to wait until other document updates are processed
-   */
-  public async updateAnnotation(document: vscode.TextDocument, updatedAnnotation: Annotation): Promise<void> {
-    console.log("Updating annotation", updatedAnnotation.id, "for document", document.uri.toString(), "with updated annotation", updatedAnnotation);
-    const documentKey = document.uri.toString();
-    const annotations = this.documentAnnotations.get(documentKey) || [];
-    const fixedUpdatedAnnotation = {
-      ...updatedAnnotation,
-      document: updatedAnnotation.document || document.getText() // Ensure the annotation's document field is updated to match the current document text
-    };
+  const editors = vscode.window.visibleTextEditors.filter(
+    (e) => e.document.uri.toString() === documentKey
+  );
+  if (editors.length === 0) {
+    return [];
+  }
 
-    // Skip identical annotation updates to avoid wasting time on decorations and saves
-    const existingAnnotation = annotations.find(a => a.id === updatedAnnotation.id);
-    if (existingAnnotation) {
-      const isIdentical = existingAnnotation.start === fixedUpdatedAnnotation.start &&
-                          existingAnnotation.end === fixedUpdatedAnnotation.end &&
-                          existingAnnotation.document === fixedUpdatedAnnotation.document &&
-        JSON.stringify(existingAnnotation.metadata) === JSON.stringify(fixedUpdatedAnnotation.metadata);
-      if (isIdentical) {
-        console.log("Skipping annotation update because it is identical to the existing annotation");
-        return;
-      }
+  const selectedAnnotationId = AnnotationManagerPanel.currentPanel?.selectedAnnotationId;
+  const docText = document.getText();
+  const result: vscode.TextEditorDecorationType[] = [];
+
+  for (const annotation of annotations) {
+    if (annotation.document !== docText) {
+      continue;
     }
-    
-    // // Update the annotation
-    // const updatedAnnotations = annotations.map(a => 
-    //   a.id === updatedAnnotation.id ? fixedUpdatedAnnotation : a
-    // );
-
-    // getUpdatedAnnotations as a function
-    const getUpdatedAnnotations = (currentDocumentText: string): Annotation[] => {
-      const annotations = this.documentAnnotations.get(documentKey) || [];
-      return annotations.map(a => 
-        a.id === updatedAnnotation.id ?
-          {
-            ...a,
-            ...updatedAnnotation,
-            document: updatedAnnotation.document || currentDocumentText // Ensure the annotation's document field is updated to match the current document text
-          } 
-        : a
-      );
-    };
-    
-    this.documentAnnotations.set(documentKey, getUpdatedAnnotations(document.getText()));
-
-    await this.saveAnnotationsForDocument(document);
-
-    // If the annotation's document text has changed, we may need to update the document on disk to match the annotation's document
-    if (updatedAnnotation.document && updatedAnnotation.document !== document.getText()) {
-      console.debug("Annotation document text differs from current document text, updating document to match annotation");
-      // Update the document text to match the annotation's document
-      const edit = new vscode.WorkspaceEdit();
-      const fullRange = new vscode.Range(
-        document.positionAt(0),
-        document.positionAt(document.getText().length)
-      );
-      edit.replace(document.uri, fullRange, updatedAnnotation.document);
-      await vscode.workspace.applyEdit(edit).then(async success => {
-        if (!success) {
-          console.error("Failed to update document text to match annotation");
-
-          // Revert the annotation update if the document update fails
-          const revertedAnnotations = annotations.map(a => 
-            a.id === updatedAnnotation.id ? {...a, document: document.getText()} : a
-          );
-          this.documentAnnotations.set(documentKey, revertedAnnotations);
-          await this.updateDecorations(document);
-          await this.notifyAnnotationsChanged(document);
-          return;
-        }
-        this.documentAnnotations.set(documentKey, getUpdatedAnnotations(document.getText()));
-        await this.saveAnnotationsForDocument(document);
-        await this.updateDecorations(document);
-        await this.notifyAnnotationsChanged(document);
-        await this.updateDecorations(document);
+    try {
+      const isSelected = selectedAnnotationId === annotation.id;
+      const baseColor = annotation.metadata?.color || "rgba(255,255,0,0.3)";
+      const decorationColor = resolveDecorationColor(baseColor, isSelected);
+      const gutterColor = resolveGutterColor(baseColor);
+
+      const startPos = document.positionAt(annotation.start);
+      const endPos = document.positionAt(annotation.end);
+      const range = new vscode.Range(startPos, endPos);
+
+      const textDecorationType = vscode.window.createTextEditorDecorationType({
+        borderColor: decorationColor,
+        borderStyle: "none none solid none",
+      });
+      const gutterDecorationType = vscode.window.createTextEditorDecorationType({
+        isWholeLine: true,
+        borderColor: gutterColor,
+        borderWidth: "3px",
+        borderStyle: "none solid none none",
       });
-      console.debug("finished updating document text to match annotation for", updatedAnnotation);
-      const updatedDoc = await vscode.workspace.openTextDocument(document.uri);
-      await this.saveAnnotationsForDocument(updatedDoc);
-      await this.updateDecorations(updatedDoc);
-      return; // Wait for the document update to trigger the annotation update through the change listener
-      // NOTE I didn't think hard about this, it might not work as expected for unusual updates.
+
+      for (const editor of editors) {
+        editor.setDecorations(textDecorationType, [range]);
+        editor.setDecorations(gutterDecorationType, [range]);
+      }
+
+      result.push(textDecorationType, gutterDecorationType);
+    } catch (error) {
+      console.error("Error creating decoration:", error);
     }
-    
-    // Update decorations and save, making sure decoration updates happen after document text is updated
-    await this.updateDecorations(document);
-    await this.saveAnnotationsForDocument(document);
-    await this.notifyAnnotationsChanged(document);
-    console.debug("Finished updating annotation", updatedAnnotation);
   }
 
-  /**
-   * Moves an annotation to a new position in the document
-   */
-  public moveAnnotation(document: vscode.TextDocument, annotationId: string, newStart: number, newEnd: number): void {
-    const documentKey = document.uri.toString();
-    const annotations = this.documentAnnotations.get(documentKey) || [];
-    
-    // Find the annotation to move
-    const annotationIndex = annotations.findIndex(a => a.id === annotationId);
-    
-    if (annotationIndex === -1) {
-      vscode.window.showErrorMessage(`Annotation with ID ${annotationId} not found.`);
+  return result;
+}
+
+
+// ═══════════════════════════════════════════════════════════════════════════════
+// Orchestration — these take TrackerState, call pure/IO functions, and write
+// back into state. They are the "outermost level" that owns state updates.
+// ═══════════════════════════════════════════════════════════════════════════════
+
+function refreshDecorationsAndNotify(state: TrackerState, document: vscode.TextDocument): void {
+  const documentKey = document.uri.toString();
+  const annotations = state.documentAnnotations.get(documentKey) || [];
+  state.decorationTypes.set(
+    documentKey,
+    rebuildDecorations(state.decorationTypes.get(documentKey), annotations, document)
+  );
+  notifyPanel(document, annotations);
+}
+
+function saveAndRefresh(state: TrackerState, document: vscode.TextDocument): void {
+  const documentKey = document.uri.toString();
+  const annotations = state.documentAnnotations.get(documentKey) || [];
+  writeAnnotationsToDisk(annotations, document);
+  refreshDecorationsAndNotify(state, document);
+}
+
+function loadAnnotationsForDocument(state: TrackerState, document: vscode.TextDocument): Annotation[] {
+  const documentKey = document.uri.toString();
+  const annotationsUri = getAnnotationsFilePath(document.uri.fsPath);
+  console.debug(`Loading annotations for ${documentKey} from ${annotationsUri}`);
+  // TODO we have only sort-of validated that diff loading works correctly.
+
+  if (state.documentAnnotations.has(documentKey)) {
+    return state.documentAnnotations.get(documentKey) as Annotation[];
+  }
+
+  const loaded = readAnnotationsFromDisk(document.uri.fsPath);
+  if (loaded !== null) {
+    state.documentAnnotations.set(documentKey, loaded);
+    refreshDecorationsAndNotify(state, document);
+    return loaded;
+  }
+
+  state.documentAnnotations.set(documentKey, []);
+  return [];
+}
+
+function processAccumulatedChanges(state: TrackerState, document: vscode.TextDocument): void {
+  const documentKey = document.uri.toString();
+  const annotations = state.documentAnnotations.get(documentKey);
+  const changes = state.pendingChanges.get(documentKey) || [];
+
+  if (!annotations || annotations.length === 0 || changes.length === 0) {
+    return;
+  }
+
+  const startingContent = state.documentContentCache.get(documentKey)!;
+  const currentContent = document.getText();
+
+  const updated = applyChangesToAnnotations(annotations, changes, startingContent, currentContent);
+  state.documentAnnotations.set(documentKey, updated);
+  saveAndRefresh(state, document);
+}
+
+function onDocumentChanged(state: TrackerState, event: vscode.TextDocumentChangeEvent): void {
+  const docKey = event.document.uri.toString();
+
+  if (!state.documentAnnotations.has(docKey)) {
+    return;
+  }
+
+  if (!state.documentContentCache.has(docKey)) {
+    state.documentContentCache.set(docKey, event.document.getText());
+    return;
+  }
+
+  const existing = state.pendingChanges.get(docKey) || [];
+  state.pendingChanges.set(docKey, [...existing, ...event.contentChanges]);
+
+  if (state.fileChangeTimers.has(docKey)) {
+    clearTimeout(state.fileChangeTimers.get(docKey)!);
+  }
+
+  state.fileChangeTimers.set(docKey, setTimeout(() => {
+    const editor = vscode.window.activeTextEditor;
+    if (!editor || editor.document.uri.toString() !== docKey) {
+      console.error("Editor not active or document not loaded", editor, editor?.document.uri.toString(), docKey);
+      state.pendingChanges.delete(docKey);
+      state.fileChangeTimers.delete(docKey);
       return;
     }
-    
-    // Create a copy of the annotation with updated positions
-    const updatedAnnotation = {
-      ...annotations[annotationIndex],
-      start: newStart,
-      end: newEnd,
-      document: document.getText() // Update document text reference
-    };
-    
-    // Update the annotation in the collection
-    const updatedAnnotations = [...annotations];
-    updatedAnnotations[annotationIndex] = updatedAnnotation;
-    this.documentAnnotations.set(documentKey, updatedAnnotations);
-    
-    // Update decorations and save
-    this.updateDecorations(document);
-    this.saveAnnotationsForDocument(document);
-    this.notifyAnnotationsChanged(document);
+
+    processAccumulatedChanges(state, editor.document);
+
+    state.documentContentCache.set(docKey, editor.document.getText());
+    state.pendingChanges.delete(docKey);
+    state.fileChangeTimers.delete(docKey);
+  }, 50));
+}
+
+function onActiveEditorChanged(state: TrackerState, editor: vscode.TextEditor | undefined): void {
+  if (!editor) { return; }
+  loadAnnotationsForDocument(state, editor.document);
+  state.documentContentCache.set(editor.document.uri.toString(), editor.document.getText());
+}
+
+function addAnnotation(state: TrackerState, document: vscode.TextDocument, annotation: Annotation): void {
+  const documentKey = document.uri.toString();
+  const annotations = state.documentAnnotations.get(documentKey) || [];
+  state.documentAnnotations.set(documentKey, [...annotations, annotation]);
+  saveAndRefresh(state, document);
+}
+
+function removeAnnotation(state: TrackerState, document: vscode.TextDocument, annotationId: string): void {
+  const documentKey = document.uri.toString();
+  const annotations = state.documentAnnotations.get(documentKey) || [];
+  const updated = annotations.filter((a) => a.id !== annotationId);
+
+  state.documentAnnotations.set(documentKey, updated);
+
+  if (updated.length === 0) {
+    deleteAnnotationsFile(document.uri.fsPath);
+    refreshDecorationsAndNotify(state, document);
+  } else {
+    saveAndRefresh(state, document);
   }
+}
 
-  /**
-   * Returns annotations for a document
-   */
-  public getAnnotationsForDocument(document: vscode.TextDocument): Annotation[] {
-    const documentKey = document.uri.toString();
-    return this.documentAnnotations.get(documentKey) || [];
+/**
+ * Step 1 of updateAnnotation: validate and build the updated list.
+ * Returns null if the update should be skipped (identical annotation).
+ */
+function buildAnnotationUpdate(
+  annotations: Annotation[],
+  updatedAnnotation: Annotation,
+  currentDocText: string
+): Annotation[] | null {
+  const fixedDoc = updatedAnnotation.document || currentDocText;
+  const existing = annotations.find((a) => a.id === updatedAnnotation.id);
+  if (existing && annotationsAreIdentical(existing, { ...updatedAnnotation, document: fixedDoc })) {
+    console.log("Skipping annotation update because it is identical to the existing annotation");
+    return null;
   }
+  return patchAnnotationInList(annotations, updatedAnnotation.id, updatedAnnotation, currentDocText);
+}
 
-  public dispose(): void {
-    // Dispose all decoration types
-    for (const types of this.decorationTypes.values()) {
-      for (const type of types) {
-        type.dispose();
-      }
-    }
-    
-    // Clear timers
-    for (const timer of this.fileChangeTimers.values()) {
-      clearTimeout(timer);
-    }
-    
-    // Dispose other resources
-    this.disposables.forEach(d => d.dispose());
-    this.disposables = [];
+/**
+ * Step 2 of updateAnnotation (only when the annotation carries new document text):
+ * apply a workspace edit to bring the editor in sync with the annotation's document.
+ */
+async function applyAnnotationDocumentEdit(
+  state: TrackerState,
+  document: vscode.TextDocument,
+  updatedAnnotation: Annotation,
+  previousAnnotations: Annotation[]
+): Promise<void> {
+  const documentKey = document.uri.toString();
+
+  console.debug("Annotation document text differs from current document text, updating document to match annotation");
+
+  const edit = new vscode.WorkspaceEdit();
+  const fullRange = new vscode.Range(
+    document.positionAt(0),
+    document.positionAt(document.getText().length)
+  );
+  edit.replace(document.uri, fullRange, updatedAnnotation.document);
+
+  const success = await vscode.workspace.applyEdit(edit);
+  if (!success) {
+    console.error("Failed to update document text to match annotation");
+    const reverted = previousAnnotations.map((a) =>
+      a.id === updatedAnnotation.id ? { ...a, document: document.getText() } : a
+    );
+    state.documentAnnotations.set(documentKey, reverted);
+    refreshDecorationsAndNotify(state, document);
+    return;
+  }
+
+  // Re-patch against the now-updated document text
+  const freshAnnotations = state.documentAnnotations.get(documentKey) || [];
+  const repatched = patchAnnotationInList(freshAnnotations, updatedAnnotation.id, updatedAnnotation, document.getText());
+  state.documentAnnotations.set(documentKey, repatched);
+  saveAndRefresh(state, document);
+
+  console.debug("finished updating document text to match annotation for", updatedAnnotation);
+  const updatedDoc = await vscode.workspace.openTextDocument(document.uri);
+  const finalAnnotations = state.documentAnnotations.get(documentKey) || [];
+  const finalPatched = patchAnnotationInList(finalAnnotations, updatedAnnotation.id, updatedAnnotation, updatedDoc.getText());
+  state.documentAnnotations.set(documentKey, finalPatched);
+  writeAnnotationsToDisk(finalPatched, updatedDoc);
+  state.decorationTypes.set(
+    documentKey,
+    rebuildDecorations(state.decorationTypes.get(documentKey), finalPatched, updatedDoc)
+  );
+}
+
+async function updateAnnotation(
+  state: TrackerState,
+  document: vscode.TextDocument,
+  updatedAnnotation: Annotation
+): Promise<void> {
+  console.log("Updating annotation", updatedAnnotation.id, "for document", document.uri.toString(), "with updated annotation", updatedAnnotation);
+  const documentKey = document.uri.toString();
+  const annotations = state.documentAnnotations.get(documentKey) || [];
+
+  // Step 1: build the update (pure)
+  const updated = buildAnnotationUpdate(annotations, updatedAnnotation, document.getText());
+  if (updated === null) {
+    return;
   }
+
+  state.documentAnnotations.set(documentKey, updated);
+  writeAnnotationsToDisk(updated, document);
+
+  // Step 2: if the annotation's document text differs, apply workspace edit
+  if (updatedAnnotation.document && updatedAnnotation.document !== document.getText()) {
+    await applyAnnotationDocumentEdit(state, document, updatedAnnotation, annotations);
+    return;
+  }
+
+  // Step 3: normal case — just refresh
+  refreshDecorationsAndNotify(state, document);
+  console.debug("Finished updating annotation", updatedAnnotation);
+}
+
+function moveAnnotation(
+  state: TrackerState,
+  document: vscode.TextDocument,
+  annotationId: string,
+  newStart: number,
+  newEnd: number
+): void {
+  const documentKey = document.uri.toString();
+  const annotations = state.documentAnnotations.get(documentKey) || [];
+
+  const index = annotations.findIndex((a) => a.id === annotationId);
+  if (index === -1) {
+    vscode.window.showErrorMessage(`Annotation with ID ${annotationId} not found.`);
+    return;
+  }
+
+  const updated = annotations.map((a, i) =>
+    i === index ? { ...a, start: newStart, end: newEnd, document: document.getText() } : a
+  );
+
+  state.documentAnnotations.set(documentKey, updated);
+  saveAndRefresh(state, document);
+}
+
+function getAnnotationsForDocument(state: TrackerState, document: vscode.TextDocument): Annotation[] {
+  return state.documentAnnotations.get(document.uri.toString()) || [];
+}
+
+
+// ═══════════════════════════════════════════════════════════════════════════════
+// Setup — creates state, wires VS Code events, returns a handle.
+// ═══════════════════════════════════════════════════════════════════════════════
+
+export interface TrackerHandle extends vscode.Disposable {
+  state: TrackerState;
+  loadAnnotationsForDocument(document: vscode.TextDocument): Promise<Annotation[]>;
+  saveAnnotationsForDocument(document: vscode.TextDocument): Promise<void>;
+  addAnnotation(document: vscode.TextDocument, annotation: Annotation): void;
+  removeAnnotation(document: vscode.TextDocument, annotationId: string): void;
+  updateAnnotation(document: vscode.TextDocument, updatedAnnotation: Annotation): Promise<void>;
+  moveAnnotation(document: vscode.TextDocument, annotationId: string, newStart: number, newEnd: number): void;
+  getAnnotationsForDocument(document: vscode.TextDocument): Annotation[];
+  updateDecorations(document: vscode.TextDocument): void;
+  dispose(): void;
+}
+
+export function createAnnotationTracker(_context: vscode.ExtensionContext): TrackerHandle {
+  const state: TrackerState = {
+    documentAnnotations: new Map(),
+    decorationTypes: new Map(),
+    fileChangeTimers: new Map(),
+    documentContentCache: new Map(),
+    pendingChanges: new Map(),
+  };
+
+  const disposables = [
+    vscode.workspace.onDidChangeTextDocument((e) => onDocumentChanged(state, e)),
+    vscode.window.onDidChangeActiveTextEditor((e) => onActiveEditorChanged(state, e)),
+  ];
+
+  if (vscode.window.activeTextEditor) {
+    loadAnnotationsForDocument(state, vscode.window.activeTextEditor.document);
+  }
+
+  return {
+    state,
+    loadAnnotationsForDocument: (doc) => Promise.resolve(loadAnnotationsForDocument(state, doc)),
+    saveAnnotationsForDocument: (doc) => { writeAnnotationsToDisk(state.documentAnnotations.get(doc.uri.toString()) || [], doc); return Promise.resolve(); },
+    addAnnotation: (doc, ann) => addAnnotation(state, doc, ann),
+    removeAnnotation: (doc, id) => removeAnnotation(state, doc, id),
+    updateAnnotation: (doc, ann) => updateAnnotation(state, doc, ann),
+    moveAnnotation: (doc, id, s, e) => moveAnnotation(state, doc, id, s, e),
+    getAnnotationsForDocument: (doc) => getAnnotationsForDocument(state, doc),
+    updateDecorations: (doc) => refreshDecorationsAndNotify(state, doc),
+    dispose() {
+      for (const types of state.decorationTypes.values()) {
+        for (const t of types) { t.dispose(); }
+      }
+      for (const timer of state.fileChangeTimers.values()) {
+        clearTimeout(timer);
+      }
+      for (const d of disposables) { d.dispose(); }
+    },
+  };
 }
\ No newline at end of file
diff --git a/vscode-extension/src/extension.ts b/vscode-extension/src/extension.ts
index 6a434da..c901ca3 100644
--- a/vscode-extension/src/extension.ts
+++ b/vscode-extension/src/extension.ts
@@ -9,7 +9,7 @@ import path from "path";
 
 // import retagUpdate from "./server/retag";
 import { SidebarProvider } from "./panels/AnnotationManagerPanel";
-import { AnnotationTracker } from "./AnnotationTracker";
+import { createAnnotationTracker, TrackerHandle } from "./AnnotationTracker";
 
 // Helper to run REST endpoints
 const runEndpointDictWithErrorHandlingOnPort = (
@@ -44,11 +44,11 @@ const runEndpointDictWithErrorHandlingOnPort = (
 };
 
 // Global annotation tracker instance
-export let annotationTracker: AnnotationTracker;
+export let annotationTracker: TrackerHandle;
 
 export function activate(context: vscode.ExtensionContext) {
   // Initialize the annotation tracker
-  annotationTracker = new AnnotationTracker(context);
+  annotationTracker = createAnnotationTracker(context);
   context.subscriptions.push(annotationTracker);
 
   // Register Sidebar Provider

From 550d05a3221b51a3c42ad1bf3a8a0f7d4f839a42 Mon Sep 17 00:00:00 2001
From: Edward Misback <misback@cs.washington.edu>
Date: Thu, 16 Apr 2026 04:56:58 -0400
Subject: [PATCH 17/22] Intermediate state of annotationtracker during refactor

---
 vscode-extension/src/AnnotationTracker.ts | 558 ++++++++++++++--------
 1 file changed, 354 insertions(+), 204 deletions(-)

diff --git a/vscode-extension/src/AnnotationTracker.ts b/vscode-extension/src/AnnotationTracker.ts
index fe4c83c..198831f 100644
--- a/vscode-extension/src/AnnotationTracker.ts
+++ b/vscode-extension/src/AnnotationTracker.ts
@@ -1,3 +1,32 @@
+/*
+
+At a high level, the update algo should be synchronous:
+    if the update is a no-op, just return the old state
+    generate just a patched annotation list
+        compute the full update, including possible modifications to the document and annotation positions for each annotation
+    effect (1): SYNCHRONOUSLY try to patch the annotation list on disk
+        if this fails, nothing to clean, just return the old state
+    if the document text needs an update
+        (2) SYNCHRONOUSLY try to patch the file on disk
+            [don't use VSCode's edit API, just write to the disk]
+            [after this synchronous chain completes, onchange may fire because we modified the document, but this is not a risk because we (need to ensure we) ignore changes that leave the file in a state identical to that pointed at by the current annotation list, which was previously synced by effect (1)]
+            if this fails and we previously patched annotations
+                clean up: SYNCHRONOUSLY revert annotations on disk -- this should (mostly) always succeed since we just wrote to it
+                just return the old state
+    now apply decorations (also synchronously)
+    finally, the disk representation of the document and annotations are in sync and align with our state, so we can safely notify the panel that there has been an update
+
+Other plans:
+
+Principle of least power: I don't want to see withAnnotations or other state constructions occuring outside of the top level. (I don't want to see withAnnotations at all, it's cruft, just explicitly construct a new state at the top level from the results of helpers.) The top level function operates on the state. Everything below the top is a helper that should only need parts of the state. It's very unlikely anything below the top is so important that it should need to return an update for every part of the state at the same time. If a function returns a piece of the state, it should have to possibly modify that piece of the state.
+Anti-corruption layer/Object parsing: we need to parse datatypes like the TextDocumentContentChangeEvent and TextEditorDecorationType into our own system rather than treating raw VSCode objects like they are part of our own state.
+Reify all effects as data: pure functions in the center compute and return __what should happen__; a thin outer shell actually does it. The core never touches I/O directly, including commands for/feedback from the editor.
+
+
+All TODOs in the file should be addressed (other than diff loading)
+
+*/
+
 import * as vscode from "vscode";
 import * as path from "path";
 import * as fs from "fs";
@@ -22,16 +51,20 @@ export interface Annotation {
 }
 
 export interface TrackerState {
-  documentAnnotations: Map<string, Annotation[]>;
-  decorationTypes: Map<string, vscode.TextEditorDecorationType[]>;
-  fileChangeTimers: Map<string, NodeJS.Timeout>;
-  documentContentCache: Map<string, string>;
-  pendingChanges: Map<string, vscode.TextDocumentContentChangeEvent[]>;
+  readonly documentAnnotations: ReadonlyMap<string, Annotation[]>;
+  // TODO convert this to a set of functions () => void that just do the disposal for each file, we aren't using the rest of these objects at all
+  readonly oldDecorationCleanupFunctions: ReadonlyMap<string, vscode.TextEditorDecorationType[]>;
+  readonly fileChangeTimers: ReadonlyMap<string, NodeJS.Timeout>;
+  // TODO eliminate this cache, it's not used 
+  readonly documentContentCache: ReadonlyMap<string, string>;
+  // TODO only store the necessary data from the content changes, not the full objects
+  readonly pendingChanges: ReadonlyMap<string, vscode.TextDocumentContentChangeEvent[]>;
 }
 
 
 // ═══════════════════════════════════════════════════════════════════════════════
 // Pure functions — exported for testing. These never touch TrackerState.
+// (Unchanged from the original.)
 // ═══════════════════════════════════════════════════════════════════════════════
 
 export function getAnnotationsFilePath(documentPath: string, createDir: boolean = false): string {
@@ -136,6 +169,7 @@ export function applyChangesToAnnotations(
     const endOffset = change.rangeOffset + change.rangeLength;
     const textLengthDiff = change.text.length - change.rangeLength;
     const isWhitespaceChange = /^\s*$/.test(change.text);
+    // TODO refactor this loop body into a separate pure function of the form `(annotation, {rangeOffset, rangeLength, text}) => updatedAnnotation` so it can be tested in isolation
 
     current = current.map((annotation) => {
       if (annotation.document !== startingContent) {
@@ -259,9 +293,28 @@ export function patchAnnotationInList(
   );
 }
 
+/**
+ * Step 1 of updateAnnotation: validate and build the updated list.
+ * Returns null if the update should be skipped (identical annotation).
+ */
+export function buildAnnotationUpdate(
+  annotations: Annotation[],
+  updatedAnnotation: Annotation,
+  currentDocText: string
+): Annotation[] | null {
+  const fixedDoc = updatedAnnotation.document || currentDocText;
+  const existing = annotations.find((a) => a.id === updatedAnnotation.id);
+  if (existing && annotationsAreIdentical(existing, { ...updatedAnnotation, document: fixedDoc })) {
+    console.log("Skipping annotation update because it is identical to the existing annotation");
+    return null;
+  }
+  return patchAnnotationInList(annotations, updatedAnnotation.id, updatedAnnotation, currentDocText);
+}
+
 
 // ═══════════════════════════════════════════════════════════════════════════════
 // I/O functions — read/write disk and VS Code APIs. No TrackerState access.
+// (Unchanged from the original.)
 // ═══════════════════════════════════════════════════════════════════════════════
 
 function readAnnotationsFromDisk(documentFsPath: string): Annotation[] | null {
@@ -396,263 +449,303 @@ function rebuildDecorations(
   return result;
 }
 
+async function applyAnnotationDocumentTextEdit(
+  document: vscode.TextDocument,
+  newText: string
+): Promise<boolean> {
+  const edit = new vscode.WorkspaceEdit();
+  const fullRange = new vscode.Range(
+    document.positionAt(0),
+    document.positionAt(document.getText().length)
+  );
+  edit.replace(document.uri, fullRange, newText);
+  return vscode.workspace.applyEdit(edit);
+}
+
 
 // ═══════════════════════════════════════════════════════════════════════════════
-// Orchestration — these take TrackerState, call pure/IO functions, and write
-// back into state. They are the "outermost level" that owns state updates.
+// Immutable state helpers. Every transition returns a new TrackerState; Maps
+// are cloned, not mutated. Object.freeze is applied at the top level (Maps
+// themselves remain structurally mutable, so correctness relies on never
+// calling .set/.delete on them outside these helpers).
 // ═══════════════════════════════════════════════════════════════════════════════
 
-function refreshDecorationsAndNotify(state: TrackerState, document: vscode.TextDocument): void {
-  const documentKey = document.uri.toString();
-  const annotations = state.documentAnnotations.get(documentKey) || [];
-  state.decorationTypes.set(
-    documentKey,
-    rebuildDecorations(state.decorationTypes.get(documentKey), annotations, document)
-  );
+function mapWith<K, V>(m: ReadonlyMap<K, V>, key: K, value: V): ReadonlyMap<K, V> {
+  const next = new Map(m);
+  next.set(key, value);
+  return next;
+}
+
+function mapWithout<K, V>(m: ReadonlyMap<K, V>, key: K): ReadonlyMap<K, V> {
+  const next = new Map(m);
+  next.delete(key);
+  return next;
+}
+
+function withAnnotations(s: TrackerState, key: string, anns: Annotation[]): TrackerState {
+  return { ...s, documentAnnotations: mapWith(s.documentAnnotations, key, anns) };
+}
+function withDecorationTypes(s: TrackerState, key: string, types: vscode.TextEditorDecorationType[]): TrackerState {
+  return { ...s, oldDecorationCleanupFunctions: mapWith(s.oldDecorationCleanupFunctions, key, types) };
+}
+function withContentCache(s: TrackerState, key: string, text: string): TrackerState {
+  return { ...s, documentContentCache: mapWith(s.documentContentCache, key, text) };
+}
+function withPendingChanges(s: TrackerState, key: string, changes: vscode.TextDocumentContentChangeEvent[]): TrackerState {
+  return { ...s, pendingChanges: mapWith(s.pendingChanges, key, changes) };
+}
+function withoutPendingChanges(s: TrackerState, key: string): TrackerState {
+  return { ...s, pendingChanges: mapWithout(s.pendingChanges, key) };
+}
+function withTimer(s: TrackerState, key: string, timer: NodeJS.Timeout): TrackerState {
+  return { ...s, fileChangeTimers: mapWith(s.fileChangeTimers, key, timer) };
+}
+function withoutTimer(s: TrackerState, key: string): TrackerState {
+  return { ...s, fileChangeTimers: mapWithout(s.fileChangeTimers, key) };
+}
+
+
+// ═══════════════════════════════════════════════════════════════════════════════
+// State transitions. Each takes a TrackerState and returns a new TrackerState.
+// Side effects (disk I/O, editor decorations, panel notifications) may happen,
+// but in-memory state is only updated via the returned value.
+// ═══════════════════════════════════════════════════════════════════════════════
+
+function refreshDecorationsAndNotify(state: TrackerState, document: vscode.TextDocument): TrackerState {
+  const key = document.uri.toString();
+  const annotations = state.documentAnnotations.get(key) || [];
+  const oldTypes = state.oldDecorationCleanupFunctions.get(key);
+  const newTypes = rebuildDecorations(oldTypes, annotations, document);
   notifyPanel(document, annotations);
+  return withDecorationTypes(state, key, newTypes);
 }
 
-function saveAndRefresh(state: TrackerState, document: vscode.TextDocument): void {
-  const documentKey = document.uri.toString();
-  const annotations = state.documentAnnotations.get(documentKey) || [];
+function saveAndRefresh(state: TrackerState, document: vscode.TextDocument): TrackerState {
+  const annotations = state.documentAnnotations.get(document.uri.toString()) || [];
   writeAnnotationsToDisk(annotations, document);
-  refreshDecorationsAndNotify(state, document);
+  return refreshDecorationsAndNotify(state, document);
 }
 
-function loadAnnotationsForDocument(state: TrackerState, document: vscode.TextDocument): Annotation[] {
-  const documentKey = document.uri.toString();
-  const annotationsUri = getAnnotationsFilePath(document.uri.fsPath);
-  console.debug(`Loading annotations for ${documentKey} from ${annotationsUri}`);
+function loadAnnotationsForDocument(state: TrackerState, document: vscode.TextDocument): TrackerState {
+  const key = document.uri.toString();
+  console.debug(`Loading annotations for ${key}`);
   // TODO we have only sort-of validated that diff loading works correctly.
-
-  if (state.documentAnnotations.has(documentKey)) {
-    return state.documentAnnotations.get(documentKey) as Annotation[];
+  if (state.documentAnnotations.has(key)) {
+    return state;
   }
-
   const loaded = readAnnotationsFromDisk(document.uri.fsPath);
   if (loaded !== null) {
-    state.documentAnnotations.set(documentKey, loaded);
-    refreshDecorationsAndNotify(state, document);
-    return loaded;
+    return refreshDecorationsAndNotify(withAnnotations(state, key, loaded), document);
   }
 
-  state.documentAnnotations.set(documentKey, []);
-  return [];
+  return withAnnotations(state, key, []);
 }
 
-function processAccumulatedChanges(state: TrackerState, document: vscode.TextDocument): void {
-  const documentKey = document.uri.toString();
-  const annotations = state.documentAnnotations.get(documentKey);
-  const changes = state.pendingChanges.get(documentKey) || [];
+function getAnnotationsForDocument(state: TrackerState, document: vscode.TextDocument): Annotation[] {
+  return state.documentAnnotations.get(document.uri.toString()) || [];
+}
 
+function processAccumulatedChanges(state: TrackerState, document: vscode.TextDocument): TrackerState {
+  const key = document.uri.toString();
+  const annotations = state.documentAnnotations.get(key);
+  const changes = state.pendingChanges.get(key) || [];
   if (!annotations || annotations.length === 0 || changes.length === 0) {
-    return;
+    return state;
   }
-
-  const startingContent = state.documentContentCache.get(documentKey)!;
+  const startingContent = annotations[0].document;
   const currentContent = document.getText();
-
   const updated = applyChangesToAnnotations(annotations, changes, startingContent, currentContent);
-  state.documentAnnotations.set(documentKey, updated);
-  saveAndRefresh(state, document);
+  return saveAndRefresh(withAnnotations(state, key, updated), document);
 }
 
-function onDocumentChanged(state: TrackerState, event: vscode.TextDocumentChangeEvent): void {
+/**
+ * Triggered by the deferred flush timer. Processes whatever changes have
+ * accumulated for `documentKey`, re-seeds the content cache, and clears the
+ * pending-changes / timer entries.
+ */
+function flushAccumulatedChanges(state: TrackerState, documentKey: string): TrackerState {
+  const editor = vscode.window.activeTextEditor;
+  if (!editor || editor.document.uri.toString() !== documentKey) {
+    console.error(
+      "Editor not active or document not loaded",
+      editor,
+      editor?.document.uri.toString(),
+      documentKey
+    );
+    return withoutTimer(withoutPendingChanges(state, documentKey), documentKey);
+  }
+  const afterProcess = processAccumulatedChanges(state, editor.document);
+  const afterCache = withContentCache(afterProcess, documentKey, editor.document.getText());
+  return withoutTimer(withoutPendingChanges(afterCache, documentKey), documentKey);
+}
+
+/**
+ * `scheduleFlush` is a narrow capability: it only lets the callee arrange for
+ * a known future transition (flushAccumulatedChanges) to run on docKey. It
+ * does NOT expose setState. The existing timer is cleared here because
+ * clearTimeout is a side effect on the OS, not a state mutation.
+ */
+function onDocumentChanged(
+  state: TrackerState,
+  event: vscode.TextDocumentChangeEvent,
+  scheduleFlush: (documentKey: string) => NodeJS.Timeout
+): TrackerState {
   const docKey = event.document.uri.toString();
 
   if (!state.documentAnnotations.has(docKey)) {
-    return;
+    return state;
   }
 
   if (!state.documentContentCache.has(docKey)) {
-    state.documentContentCache.set(docKey, event.document.getText());
-    return;
+    return withContentCache(state, docKey, event.document.getText());
   }
 
-  const existing = state.pendingChanges.get(docKey) || [];
-  state.pendingChanges.set(docKey, [...existing, ...event.contentChanges]);
+  const existingChanges = state.pendingChanges.get(docKey) || [];
+  const nextChanges = [...existingChanges, ...event.contentChanges];
 
-  if (state.fileChangeTimers.has(docKey)) {
-    clearTimeout(state.fileChangeTimers.get(docKey)!);
+  const existingTimer = state.fileChangeTimers.get(docKey);
+  if (existingTimer) {
+    clearTimeout(existingTimer);
   }
+  const newTimer = scheduleFlush(docKey);
 
-  state.fileChangeTimers.set(docKey, setTimeout(() => {
-    const editor = vscode.window.activeTextEditor;
-    if (!editor || editor.document.uri.toString() !== docKey) {
-      console.error("Editor not active or document not loaded", editor, editor?.document.uri.toString(), docKey);
-      state.pendingChanges.delete(docKey);
-      state.fileChangeTimers.delete(docKey);
-      return;
-    }
-
-    processAccumulatedChanges(state, editor.document);
-
-    state.documentContentCache.set(docKey, editor.document.getText());
-    state.pendingChanges.delete(docKey);
-    state.fileChangeTimers.delete(docKey);
-  }, 50));
+  return withTimer(withPendingChanges(state, docKey, nextChanges), docKey, newTimer);
 }
 
-function onActiveEditorChanged(state: TrackerState, editor: vscode.TextEditor | undefined): void {
-  if (!editor) { return; }
-  loadAnnotationsForDocument(state, editor.document);
-  state.documentContentCache.set(editor.document.uri.toString(), editor.document.getText());
+function onActiveEditorChanged(
+  state: TrackerState,
+  editor: vscode.TextEditor | undefined
+): TrackerState {
+  if (!editor) {
+    return state;
+  }
+  const afterLoad = loadAnnotationsForDocument(state, editor.document);
+  return withContentCache(afterLoad, editor.document.uri.toString(), editor.document.getText());
 }
 
-function addAnnotation(state: TrackerState, document: vscode.TextDocument, annotation: Annotation): void {
-  const documentKey = document.uri.toString();
-  const annotations = state.documentAnnotations.get(documentKey) || [];
-  state.documentAnnotations.set(documentKey, [...annotations, annotation]);
-  saveAndRefresh(state, document);
+function addAnnotation(
+  state: TrackerState,
+  document: vscode.TextDocument,
+  annotation: Annotation
+): TrackerState {
+  const key = document.uri.toString();
+  const annotations = state.documentAnnotations.get(key) || [];
+  return saveAndRefresh(withAnnotations(state, key, [...annotations, annotation]), document);
 }
 
-function removeAnnotation(state: TrackerState, document: vscode.TextDocument, annotationId: string): void {
-  const documentKey = document.uri.toString();
-  const annotations = state.documentAnnotations.get(documentKey) || [];
+function removeAnnotation(
+  state: TrackerState,
+  document: vscode.TextDocument,
+  annotationId: string
+): TrackerState {
+  const key = document.uri.toString();
+  const annotations = state.documentAnnotations.get(key) || [];
   const updated = annotations.filter((a) => a.id !== annotationId);
-
-  state.documentAnnotations.set(documentKey, updated);
-
+  const next = withAnnotations(state, key, updated);
   if (updated.length === 0) {
     deleteAnnotationsFile(document.uri.fsPath);
-    refreshDecorationsAndNotify(state, document);
-  } else {
-    saveAndRefresh(state, document);
-  }
-}
-
-/**
- * Step 1 of updateAnnotation: validate and build the updated list.
- * Returns null if the update should be skipped (identical annotation).
- */
-function buildAnnotationUpdate(
-  annotations: Annotation[],
-  updatedAnnotation: Annotation,
-  currentDocText: string
-): Annotation[] | null {
-  const fixedDoc = updatedAnnotation.document || currentDocText;
-  const existing = annotations.find((a) => a.id === updatedAnnotation.id);
-  if (existing && annotationsAreIdentical(existing, { ...updatedAnnotation, document: fixedDoc })) {
-    console.log("Skipping annotation update because it is identical to the existing annotation");
-    return null;
+    return refreshDecorationsAndNotify(next, document);
   }
-  return patchAnnotationInList(annotations, updatedAnnotation.id, updatedAnnotation, currentDocText);
+  return saveAndRefresh(next, document);
 }
 
-/**
- * Step 2 of updateAnnotation (only when the annotation carries new document text):
- * apply a workspace edit to bring the editor in sync with the annotation's document.
- */
-async function applyAnnotationDocumentEdit(
+function moveAnnotation(
   state: TrackerState,
   document: vscode.TextDocument,
-  updatedAnnotation: Annotation,
-  previousAnnotations: Annotation[]
-): Promise<void> {
-  const documentKey = document.uri.toString();
-
-  console.debug("Annotation document text differs from current document text, updating document to match annotation");
-
-  const edit = new vscode.WorkspaceEdit();
-  const fullRange = new vscode.Range(
-    document.positionAt(0),
-    document.positionAt(document.getText().length)
+  annotationId: string,
+  newStart: number,
+  newEnd: number
+): TrackerState {
+  const key = document.uri.toString();
+  const annotations = state.documentAnnotations.get(key) || [];
+  const index = annotations.findIndex((a) => a.id === annotationId);
+  if (index === -1) {
+    vscode.window.showErrorMessage(`Annotation with ID ${annotationId} not found.`);
+    return state;
+  }
+  const updated = annotations.map((a, i) =>
+    i === index ? { ...a, start: newStart, end: newEnd, document: document.getText() } : a
   );
-  edit.replace(document.uri, fullRange, updatedAnnotation.document);
+  return saveAndRefresh(withAnnotations(state, key, updated), document);
+}
 
-  const success = await vscode.workspace.applyEdit(edit);
-  if (!success) {
-    console.error("Failed to update document text to match annotation");
-    const reverted = previousAnnotations.map((a) =>
-      a.id === updatedAnnotation.id ? { ...a, document: document.getText() } : a
-    );
-    state.documentAnnotations.set(documentKey, reverted);
-    refreshDecorationsAndNotify(state, document);
-    return;
-  }
 
-  // Re-patch against the now-updated document text
-  const freshAnnotations = state.documentAnnotations.get(documentKey) || [];
-  const repatched = patchAnnotationInList(freshAnnotations, updatedAnnotation.id, updatedAnnotation, document.getText());
-  state.documentAnnotations.set(documentKey, repatched);
-  saveAndRefresh(state, document);
-
-  console.debug("finished updating document text to match annotation for", updatedAnnotation);
-  const updatedDoc = await vscode.workspace.openTextDocument(document.uri);
-  const finalAnnotations = state.documentAnnotations.get(documentKey) || [];
-  const finalPatched = patchAnnotationInList(finalAnnotations, updatedAnnotation.id, updatedAnnotation, updatedDoc.getText());
-  state.documentAnnotations.set(documentKey, finalPatched);
-  writeAnnotationsToDisk(finalPatched, updatedDoc);
-  state.decorationTypes.set(
-    documentKey,
-    rebuildDecorations(state.decorationTypes.get(documentKey), finalPatched, updatedDoc)
-  );
+// ─── updateAnnotation phases ──────────────────────────────────────────────────
+// updateAnnotation has an async workspace-edit step that may race with other
+// events. To preserve the original's "re-read state after each await" behavior
+// without leaking getState/setState into the helper, the async orchestration
+// lives in the returned method of createAnnotationTracker; each phase below is
+// a pure state transition invoked between awaits.
+
+interface UpdateBeginResult {
+  nextState: TrackerState;
+  needsDocumentEdit: boolean;
+  skipped: boolean;
 }
 
-async function updateAnnotation(
+function beginAnnotationUpdate(
   state: TrackerState,
   document: vscode.TextDocument,
   updatedAnnotation: Annotation
-): Promise<void> {
-  console.log("Updating annotation", updatedAnnotation.id, "for document", document.uri.toString(), "with updated annotation", updatedAnnotation);
-  const documentKey = document.uri.toString();
-  const annotations = state.documentAnnotations.get(documentKey) || [];
-
-  // Step 1: build the update (pure)
+): UpdateBeginResult {
+  console.log(
+    "Updating annotation", updatedAnnotation.id,
+    "for document", document.uri.toString(),
+    "with updated annotation", updatedAnnotation
+  );
+  const key = document.uri.toString();
+  const annotations = state.documentAnnotations.get(key) || [];
   const updated = buildAnnotationUpdate(annotations, updatedAnnotation, document.getText());
   if (updated === null) {
-    return;
+    return { nextState: state, needsDocumentEdit: false, skipped: true };
   }
-
-  state.documentAnnotations.set(documentKey, updated);
   writeAnnotationsToDisk(updated, document);
-
-  // Step 2: if the annotation's document text differs, apply workspace edit
-  if (updatedAnnotation.document && updatedAnnotation.document !== document.getText()) {
-    await applyAnnotationDocumentEdit(state, document, updatedAnnotation, annotations);
-    return;
-  }
-
-  // Step 3: normal case — just refresh
-  refreshDecorationsAndNotify(state, document);
-  console.debug("Finished updating annotation", updatedAnnotation);
+  const needsDocumentEdit =
+    !!updatedAnnotation.document && updatedAnnotation.document !== document.getText();
+  return {
+    nextState: withAnnotations(state, key, updated),
+    needsDocumentEdit,
+    skipped: false,
+  };
 }
 
-function moveAnnotation(
+function completeAnnotationUpdateAfterEdit(
   state: TrackerState,
   document: vscode.TextDocument,
-  annotationId: string,
-  newStart: number,
-  newEnd: number
-): void {
-  const documentKey = document.uri.toString();
-  const annotations = state.documentAnnotations.get(documentKey) || [];
-
-  const index = annotations.findIndex((a) => a.id === annotationId);
-  if (index === -1) {
-    vscode.window.showErrorMessage(`Annotation with ID ${annotationId} not found.`);
-    return;
-  }
-
-  const updated = annotations.map((a, i) =>
-    i === index ? { ...a, start: newStart, end: newEnd, document: document.getText() } : a
+  updatedAnnotation: Annotation
+): TrackerState {
+  const key = document.uri.toString();
+  const annotations = state.documentAnnotations.get(key) || [];
+  const repatched = patchAnnotationInList(
+    annotations,
+    updatedAnnotation.id,
+    updatedAnnotation,
+    document.getText()
   );
-
-  state.documentAnnotations.set(documentKey, updated);
-  saveAndRefresh(state, document);
+  return saveAndRefresh(withAnnotations(state, key, repatched), document);
 }
 
-function getAnnotationsForDocument(state: TrackerState, document: vscode.TextDocument): Annotation[] {
-  return state.documentAnnotations.get(document.uri.toString()) || [];
+function revertAnnotationUpdate(
+  state: TrackerState,
+  document: vscode.TextDocument,
+  updatedAnnotation: Annotation
+): TrackerState {
+  console.error("Failed to update document text to match annotation");
+  const key = document.uri.toString();
+  const annotations = state.documentAnnotations.get(key) || [];
+  const reverted = annotations.map((a) =>
+    a.id === updatedAnnotation.id ? { ...a, document: document.getText() } : a
+  );
+  return refreshDecorationsAndNotify(withAnnotations(state, key, reverted), document);
 }
 
 
 // ═══════════════════════════════════════════════════════════════════════════════
-// Setup — creates state, wires VS Code events, returns a handle.
+// createAnnotationTracker — the only place that owns state.
 // ═══════════════════════════════════════════════════════════════════════════════
 
 export interface TrackerHandle extends vscode.Disposable {
-  state: TrackerState;
+  readonly state: Readonly<TrackerState>;
   loadAnnotationsForDocument(document: vscode.TextDocument): Promise<Annotation[]>;
   saveAnnotationsForDocument(document: vscode.TextDocument): Promise<void>;
   addAnnotation(document: vscode.TextDocument, annotation: Annotation): void;
@@ -665,38 +758,95 @@ export interface TrackerHandle extends vscode.Disposable {
 }
 
 export function createAnnotationTracker(_context: vscode.ExtensionContext): TrackerHandle {
-  const state: TrackerState = {
+  let state: Readonly<TrackerState> = {
     documentAnnotations: new Map(),
-    decorationTypes: new Map(),
+    oldDecorationCleanupFunctions: new Map(),
     fileChangeTimers: new Map(),
     documentContentCache: new Map(),
     pendingChanges: new Map(),
   };
 
+  const getState = (): TrackerState => state;
+  const setState = (next: TrackerState): void => { state = next; };
+
+  // Narrow capability handed to onDocumentChanged. Not setState — only the
+  // ability to schedule a known future transition on a known docKey.
+  const scheduleFlush = (docKey: string): NodeJS.Timeout =>
+    setTimeout(() => setState(flushAccumulatedChanges(getState(), docKey)), 50);
+
   const disposables = [
-    vscode.workspace.onDidChangeTextDocument((e) => onDocumentChanged(state, e)),
-    vscode.window.onDidChangeActiveTextEditor((e) => onActiveEditorChanged(state, e)),
+    vscode.workspace.onDidChangeTextDocument((e) =>
+      setState(onDocumentChanged(getState(), e, scheduleFlush))
+    ),
+    vscode.window.onDidChangeActiveTextEditor((editor) =>
+      setState(onActiveEditorChanged(getState(), editor))
+    ),
   ];
 
-  if (vscode.window.activeTextEditor) {
-    loadAnnotationsForDocument(state, vscode.window.activeTextEditor.document);
-  }
+  // Initial load. No conditional here — onActiveEditorChanged handles the
+  // undefined-editor case internally.
+  setState(onActiveEditorChanged(getState(), vscode.window.activeTextEditor));
 
   return {
-    state,
-    loadAnnotationsForDocument: (doc) => Promise.resolve(loadAnnotationsForDocument(state, doc)),
-    saveAnnotationsForDocument: (doc) => { writeAnnotationsToDisk(state.documentAnnotations.get(doc.uri.toString()) || [], doc); return Promise.resolve(); },
-    addAnnotation: (doc, ann) => addAnnotation(state, doc, ann),
-    removeAnnotation: (doc, id) => removeAnnotation(state, doc, id),
-    updateAnnotation: (doc, ann) => updateAnnotation(state, doc, ann),
-    moveAnnotation: (doc, id, s, e) => moveAnnotation(state, doc, id, s, e),
-    getAnnotationsForDocument: (doc) => getAnnotationsForDocument(state, doc),
-    updateDecorations: (doc) => refreshDecorationsAndNotify(state, doc),
+    get state() { return getState(); },
+
+    loadAnnotationsForDocument: async (doc) => {
+      setState(loadAnnotationsForDocument(getState(), doc));
+      return getAnnotationsForDocument(getState(), doc);
+    },
+
+    saveAnnotationsForDocument: async (doc) => {
+      writeAnnotationsToDisk(getAnnotationsForDocument(getState(), doc), doc);
+    },
+
+    addAnnotation: (doc, ann) => setState(addAnnotation(getState(), doc, ann)),
+
+    removeAnnotation: (doc, id) => setState(removeAnnotation(getState(), doc, id)),
+
+    updateAnnotation: async (doc, ann) => {
+      // Phase 1: sync validate + patch + write.
+      const { nextState, needsDocumentEdit, skipped } = beginAnnotationUpdate(getState(), doc, ann);
+      if (skipped) { return; }
+      setState(nextState);
+
+      // Phase 2a: no workspace edit required — just refresh decorations.
+      if (!needsDocumentEdit) {
+        setState(refreshDecorationsAndNotify(getState(), doc));
+        console.debug("Finished updating annotation", ann);
+        return;
+      }
+
+      // Phase 2b: apply workspace edit. Each await re-reads state afterwards
+      // via getState() so we survive concurrent mutations.
+      console.debug("Annotation document text differs from current; applying workspace edit");
+      const success = await applyAnnotationDocumentTextEdit(doc, ann.document);
+      if (!success) {
+        setState(revertAnnotationUpdate(getState(), doc, ann));
+        return;
+      }
+
+      setState(completeAnnotationUpdateAfterEdit(getState(), doc, ann));
+
+      // Re-open the document to pick up any normalization vscode may have done
+      // (line endings, etc.) and patch one more time against that canonical text.
+      const updatedDoc = await vscode.workspace.openTextDocument(doc.uri);
+      setState(completeAnnotationUpdateAfterEdit(getState(), updatedDoc, ann));
+
+      console.debug("Finished updating annotation", ann);
+    },
+
+    moveAnnotation: (doc, id, start, end) => setState(moveAnnotation(getState(), doc, id, start, end)),
+
+    getAnnotationsForDocument: (doc) => getAnnotationsForDocument(getState(), doc),
+
+    updateDecorations: (doc) => setState(refreshDecorationsAndNotify(getState(), doc)),
+
     dispose() {
-      for (const types of state.decorationTypes.values()) {
+      const finalState = getState();
+      for (const types of finalState.oldDecorationCleanupFunctions.values()) {
         for (const t of types) { t.dispose(); }
       }
-      for (const timer of state.fileChangeTimers.values()) {
+      for (const timer of finalState.fileChangeTimers.values()) {
         clearTimeout(timer);
       }
       for (const d of disposables) { d.dispose(); }

From 12c5a2a49ef80c5d2b419a1e4a62d81c28a41121 Mon Sep 17 00:00:00 2001
From: Edward Misback <misback@cs.washington.edu>
Date: Thu, 16 Apr 2026 05:29:45 -0400
Subject: [PATCH 18/22] Another intermediate update (pre-prompt).

---
 vscode-extension/src/AnnotationTracker.ts | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/vscode-extension/src/AnnotationTracker.ts b/vscode-extension/src/AnnotationTracker.ts
index 198831f..51814e4 100644
--- a/vscode-extension/src/AnnotationTracker.ts
+++ b/vscode-extension/src/AnnotationTracker.ts
@@ -18,7 +18,7 @@ At a high level, the update algo should be synchronous:
 
 Other plans:
 
-Principle of least power: I don't want to see withAnnotations or other state constructions occuring outside of the top level. (I don't want to see withAnnotations at all, it's cruft, just explicitly construct a new state at the top level from the results of helpers.) The top level function operates on the state. Everything below the top is a helper that should only need parts of the state. It's very unlikely anything below the top is so important that it should need to return an update for every part of the state at the same time. If a function returns a piece of the state, it should have to possibly modify that piece of the state.
+Principle of minimal interface: I don't want to see withAnnotations or other state constructions occuring outside of the top level. (I don't want to see withAnnotations at all, it's cruft, just explicitly construct a new state at the top level from the results of helpers.) The top level function operates on the state. Everything below the top is a helper that should only need parts of the state. It's very unlikely anything below the top is so important that it should need to return an update for every part of the state at the same time. If a function returns a piece of the state, it should have to possibly modify that piece of the state.
 Anti-corruption layer/Object parsing: we need to parse datatypes like the TextDocumentContentChangeEvent and TextEditorDecorationType into our own system rather than treating raw VSCode objects like they are part of our own state.
 Reify all effects as data: pure functions in the center compute and return __what should happen__; a thin outer shell actually does it. The core never touches I/O directly, including commands for/feedback from the editor.
 

From 0683ba37084b260caad8b15e2ef53bf2788019bc Mon Sep 17 00:00:00 2001
From: Edward Misback <misback@cs.washington.edu>
Date: Thu, 16 Apr 2026 07:02:56 -0400
Subject: [PATCH 19/22] Trying synchronous file updates for now.

---
 vscode-extension/src/AnnotationTracker.ts | 1146 +++++++++++----------
 1 file changed, 599 insertions(+), 547 deletions(-)

diff --git a/vscode-extension/src/AnnotationTracker.ts b/vscode-extension/src/AnnotationTracker.ts
index 51814e4..fead001 100644
--- a/vscode-extension/src/AnnotationTracker.ts
+++ b/vscode-extension/src/AnnotationTracker.ts
@@ -1,29 +1,34 @@
 /*
 
-At a high level, the update algo should be synchronous:
-    if the update is a no-op, just return the old state
-    generate just a patched annotation list
-        compute the full update, including possible modifications to the document and annotation positions for each annotation
-    effect (1): SYNCHRONOUSLY try to patch the annotation list on disk
-        if this fails, nothing to clean, just return the old state
-    if the document text needs an update
-        (2) SYNCHRONOUSLY try to patch the file on disk
-            [don't use VSCode's edit API, just write to the disk]
-            [after this synchronous chain completes, onchange may fire because we modified the document, but this is not a risk because we (need to ensure we) ignore changes that leave the file in a state identical to that pointed at by the current annotation list, which was previously synced by effect (1)]
-            if this fails and we previously patched annotations
-                clean up: SYNCHRONOUSLY revert annotations on disk -- this should (mostly) always succeed since we just wrote to it
-                just return the old state
-    now apply decorations (also synchronously)
-    finally, the disk representation of the document and annotations are in sync and align with our state, so we can safely notify the panel that there has been an update
-
-Other plans:
-
-Principle of minimal interface: I don't want to see withAnnotations or other state constructions occuring outside of the top level. (I don't want to see withAnnotations at all, it's cruft, just explicitly construct a new state at the top level from the results of helpers.) The top level function operates on the state. Everything below the top is a helper that should only need parts of the state. It's very unlikely anything below the top is so important that it should need to return an update for every part of the state at the same time. If a function returns a piece of the state, it should have to possibly modify that piece of the state.
-Anti-corruption layer/Object parsing: we need to parse datatypes like the TextDocumentContentChangeEvent and TextEditorDecorationType into our own system rather than treating raw VSCode objects like they are part of our own state.
-Reify all effects as data: pure functions in the center compute and return __what should happen__; a thin outer shell actually does it. The core never touches I/O directly, including commands for/feedback from the editor.
-
-
-All TODOs in the file should be addressed (other than diff loading)
+Synchronous update algorithm:
+  - If the update is a no-op, return the old state.
+  - Compute a plan: a new annotation list plus optional new document text.
+  - Effect (1): SYNCHRONOUSLY write the annotation list to disk.
+      If it fails, there's nothing to clean up — return the old state.
+  - If the document text needs to change:
+    - Effect (2): SYNCHRONOUSLY write the new document text with fs.writeFileSync
+      (NOT VSCode's edit API).
+      If it fails, SYNCHRONOUSLY revert the annotation file and return the old state.
+    - After this completes, VSCode's file watcher may fire onchange. That's fine:
+      applyChangesToAnnotations short-circuits when startingContent === currentContent,
+      which it will be because we just patched both.
+  - Apply decorations synchronously.
+  - Notify the panel.
+
+Design principles (from the original header):
+
+  1. Minimal interface. No withAnnotations / withDecorationTypes / etc. cruft.
+     State construction happens only at the top level of createAnnotationTracker.
+     Helpers take the pieces of state they need and return just what they modify.
+
+  2. Anti-corruption layer. VSCode types like TextDocumentContentChangeEvent and
+     TextEditorDecorationType are parsed at the edge into our own domain types
+     (ContentChange, DecorationDisposer, DecorationSpec) before entering the core.
+
+  3. Reify all effects as data, all the way down. The pure core computes plans
+     (AnnotationUpdatePlan, DecorationSpec[]) describing what should happen. The
+     thin shell in createAnnotationTracker executes them. The core never touches
+     I/O or VSCode APIs.
 
 */
 
@@ -33,6 +38,11 @@ import * as fs from "fs";
 import { createPatch, applyPatch } from "diff";
 import { AnnotationManagerPanel } from "./panels/AnnotationManagerPanel";
 
+
+// ═══════════════════════════════════════════════════════════════════════════════
+// Domain types.
+// ═══════════════════════════════════════════════════════════════════════════════
+
 export interface Annotation {
   // HACK this just duplicates "../webview-ui/src/Annotation.tsx"
   id: string;
@@ -50,21 +60,55 @@ export interface Annotation {
   };
 }
 
-export interface TrackerState {
-  readonly documentAnnotations: ReadonlyMap<string, Annotation[]>;
-  // TODO convert this to a set of functions () => void that just do the disposal for each file, we aren't using the rest of these objects at all
-  readonly oldDecorationCleanupFunctions: ReadonlyMap<string, vscode.TextEditorDecorationType[]>;
-  readonly fileChangeTimers: ReadonlyMap<string, NodeJS.Timeout>;
-  // TODO eliminate this cache, it's not used 
-  readonly documentContentCache: ReadonlyMap<string, string>;
-  // TODO only store the necessary data from the content changes, not the full objects
-  readonly pendingChanges: ReadonlyMap<string, vscode.TextDocumentContentChangeEvent[]>;
+type AnnotationUpdate = Annotation & {
+  settingAnchorTextOnly?: boolean; // if true, only update the annotation's text, not its full document
+};
+
+/** Anti-corruption: parsed form of vscode.TextDocumentContentChangeEvent. */
+export interface ContentChange {
+  readonly rangeOffset: number;
+  readonly rangeLength: number;
+  readonly text: string;
 }
 
+/** Anti-corruption: a DecorationType collapsed down to just the capability we use. */
+export type DecorationDisposer = () => void;
+
+/**
+ * Anti-corruption: a pure description of a decoration to apply. The shell turns
+ * this into vscode.TextEditorDecorationType instances and Range objects.
+ */
+export interface DecorationSpec {
+  readonly annotationId: string;
+  readonly startOffset: number;
+  readonly endOffset: number;
+  readonly textBorderColor: string;
+  readonly gutterBorderColor: string;
+}
+
+type DocumentKey = string; // document URI as string
+
+export interface TrackerState {
+  readonly documentAnnotations: ReadonlyMap<DocumentKey, Annotation[]>;
+  // TODO don't need an array, just a single disposer per annotation file
+  readonly decorationDisposers: ReadonlyMap<DocumentKey, DecorationDisposer[]>;
+  readonly fileChangeTimers: ReadonlyMap<DocumentKey, NodeJS.Timeout>;
+  readonly pendingChanges: ReadonlyMap<DocumentKey, ContentChange[]>;
+}
+
+/** Plan returned by planAnnotationUpdate: the reified effect of an update. */
+export type AnnotationUpdatePlan =
+  | { readonly kind: "noop" }
+  | {
+      readonly kind: "update";
+      readonly newAnnotations: Annotation[];
+      /** non-null iff the document text on disk needs to change */
+      readonly newDocumentText: string | null;
+    };
+
 
 // ═══════════════════════════════════════════════════════════════════════════════
-// Pure functions — exported for testing. These never touch TrackerState.
-// (Unchanged from the original.)
+// Pure functions — exported for testing. No I/O, no VSCode API, no TrackerState.
 // ═══════════════════════════════════════════════════════════════════════════════
 
 export function getAnnotationsFilePath(documentPath: string, createDir: boolean = false): string {
@@ -152,87 +196,120 @@ export function serializeAnnotationsForDisk(
   return { document: globalDocument, annotations: serialized };
 }
 
-export function applyChangesToAnnotations(
-  annotations: Annotation[],
-  changes: readonly vscode.TextDocumentContentChangeEvent[],
-  startingContent: string,
-  currentContent: string
-): Annotation[] {
-  if (startingContent === currentContent) {
-    return annotations;
+/** Anti-corruption: parse a VSCode change event into our domain type. */
+export function parseContentChange(event: vscode.TextDocumentContentChangeEvent): ContentChange {
+  return {
+    rangeOffset: event.rangeOffset,
+    rangeLength: event.rangeLength,
+    text: event.text,
+  };
+}
+
+/**
+ * Apply a single content change to a single annotation. Pure; testable in
+ * isolation. Annotations whose document doesn't match the starting content are
+ * passed through unchanged.
+ */
+export function applyChangeToAnnotation(
+  annotation: Annotation,
+  change: ContentChange,
+  startingContent: string
+): Annotation {
+  if (annotation.document !== startingContent) {
+    return annotation;
   }
 
-  let current = annotations;
+  const startOffset = change.rangeOffset;
+  const endOffset = change.rangeOffset + change.rangeLength;
+  const textLengthDiff = change.text.length - change.rangeLength;
+  const isWhitespaceChange = /^\s*$/.test(change.text);
 
-  for (const change of changes) {
-    const startOffset = change.rangeOffset;
-    const endOffset = change.rangeOffset + change.rangeLength;
-    const textLengthDiff = change.text.length - change.rangeLength;
-    const isWhitespaceChange = /^\s*$/.test(change.text);
-    // TODO refactor this loop body into a separate pure function of the form `(annotation, {rangeOffset, rangeLength, text}) => updatedAnnotation` so it can be tested in isolation
-
-    current = current.map((annotation) => {
-      if (annotation.document !== startingContent) {
-        return annotation;
-      }
+  // CASE 1: Change is completely before the annotation
+  if (endOffset < annotation.start) {
+    return {
+      ...annotation,
+      start: annotation.start + textLengthDiff,
+      end: annotation.end + textLengthDiff,
+    };
+  }
 
-      // CASE 1: Change is completely before the annotation
-      if (endOffset < annotation.start) {
-        return { ...annotation, start: annotation.start + textLengthDiff, end: annotation.end + textLengthDiff };
-      }
+  // CASE 2: Change is completely after the annotation
+  if (startOffset > annotation.end) {
+    return annotation;
+  }
 
-      // CASE 2: Change is completely after the annotation
-      if (startOffset > annotation.end) {
-        return annotation;
-      }
+  // CASE 3: Change is adjacent to the annotation (immediately before)
+  if (endOffset === annotation.start) {
+    if (!isWhitespaceChange) {
+      return { ...annotation, start: startOffset, end: annotation.end + textLengthDiff };
+    }
+    return {
+      ...annotation,
+      start: annotation.start + textLengthDiff,
+      end: annotation.end + textLengthDiff,
+    };
+  }
 
-      // CASE 3: Change is adjacent to the annotation (immediately before)
-      if (endOffset === annotation.start) {
-        if (!isWhitespaceChange) {
-          return { ...annotation, start: startOffset, end: annotation.end + textLengthDiff };
-        }
-        return { ...annotation, start: annotation.start + textLengthDiff, end: annotation.end + textLengthDiff };
-      }
+  // CASE 4: Change is adjacent to the annotation (immediately after)
+  if (startOffset === annotation.end) {
+    if (!isWhitespaceChange) {
+      return { ...annotation, end: annotation.end + change.text.length };
+    }
+    return annotation;
+  }
 
-      // CASE 4: Change is adjacent to the annotation (immediately after)
-      if (startOffset === annotation.end) {
-        if (!isWhitespaceChange) {
-          return { ...annotation, end: annotation.end + change.text.length };
-        }
-        return annotation;
-      }
+  // CASE 5: Change is completely inside the annotation
+  if (startOffset >= annotation.start && endOffset <= annotation.end) {
+    return { ...annotation, end: annotation.end + textLengthDiff };
+  }
 
-      // CASE 5: Change is completely inside the annotation
-      if (startOffset >= annotation.start && endOffset <= annotation.end) {
-        return { ...annotation, end: annotation.end + textLengthDiff };
-      }
+  // CASE 6: Change partially overlaps with the start of the annotation
+  if (startOffset < annotation.start && endOffset > annotation.start && endOffset <= annotation.end) {
+    if (isWhitespaceChange) {
+      return {
+        ...annotation,
+        start: startOffset + change.text.length,
+        end: annotation.end + textLengthDiff,
+      };
+    }
+    return { ...annotation, start: startOffset, end: annotation.end + textLengthDiff };
+  }
 
-      // CASE 6: Change partially overlaps with the start of the annotation
-      if (startOffset < annotation.start && endOffset > annotation.start && endOffset <= annotation.end) {
-        if (isWhitespaceChange) {
-          return { ...annotation, start: startOffset + change.text.length, end: annotation.end + textLengthDiff };
-        }
-        return { ...annotation, start: startOffset, end: annotation.end + textLengthDiff };
-      }
+  // CASE 7: Change partially overlaps with the end of the annotation
+  if (startOffset >= annotation.start && startOffset < annotation.end && endOffset > annotation.end) {
+    if (isWhitespaceChange) {
+      return { ...annotation, end: startOffset };
+    }
+    return { ...annotation, end: startOffset + change.text.length };
+  }
 
-      // CASE 7: Change partially overlaps with the end of the annotation
-      if (startOffset >= annotation.start && startOffset < annotation.end && endOffset > annotation.end) {
-        if (isWhitespaceChange) {
-          return { ...annotation, end: startOffset };
-        }
-        return { ...annotation, end: startOffset + change.text.length };
-      }
+  // CASE 8: Change completely contains the annotation
+  if (startOffset < annotation.start && endOffset > annotation.end) {
+    if (change.text.length === 0 || isWhitespaceChange) {
+      return { ...annotation, start: startOffset, end: startOffset };
+    }
+    return { ...annotation, start: startOffset, end: startOffset + change.text.length };
+  }
 
-      // CASE 8: Change completely contains the annotation
-      if (startOffset < annotation.start && endOffset > annotation.end) {
-        if (change.text.length === 0 || isWhitespaceChange) {
-          return { ...annotation, start: startOffset, end: startOffset };
-        }
-        return { ...annotation, start: startOffset, end: startOffset + change.text.length };
-      }
+  return annotation;
+}
 
-      return annotation;
-    });
+export function applyChangesToAnnotations(
+  annotations: Annotation[],
+  changes: readonly ContentChange[],
+  startingContent: string,
+  currentContent: string
+): Annotation[] {
+  // Short-circuit: if the document's net content is what the annotations already
+  // reflect, there's nothing to do. This is what lets the synchronous update
+  // algorithm safely ignore VSCode's onchange events after we write to disk.
+  if (startingContent === currentContent) {
+    return annotations;
+  }
+
+  let current = annotations;
+  for (const change of changes) {
+    current = current.map((a) => applyChangeToAnnotation(a, change, startingContent));
   }
 
   return current.map((ann) =>
@@ -278,43 +355,70 @@ export function annotationsAreIdentical(a: Annotation, b: Annotation): boolean {
 }
 
 /**
- * Returns a new annotations list with one annotation replaced by a patched version.
+ * Pure: compute the decoration specs for a list of annotations against a given
+ * document text. Annotations whose document doesn't match are skipped.
  */
-export function patchAnnotationInList(
+export function computeDecorationSpecs(
   annotations: Annotation[],
-  annotationId: string,
-  patch: Partial<Annotation>,
-  fallbackDocument: string
-): Annotation[] {
-  return annotations.map((a) =>
-    a.id === annotationId
-      ? { ...a, ...patch, document: patch.document || fallbackDocument }
-      : a
-  );
+  documentText: string,
+  selectedAnnotationId: string | undefined
+): DecorationSpec[] {
+  const specs: DecorationSpec[] = [];
+  for (const ann of annotations) {
+    if (ann.document !== documentText) {
+      continue;
+    }
+    const isSelected = selectedAnnotationId === ann.id;
+    const baseColor = ann.metadata?.color || "rgba(255,255,0,0.3)";
+    specs.push({
+      annotationId: ann.id,
+      startOffset: ann.start,
+      endOffset: ann.end,
+      textBorderColor: resolveDecorationColor(baseColor, isSelected),
+      gutterBorderColor: resolveGutterColor(baseColor),
+    });
+  }
+  return specs;
 }
 
 /**
- * Step 1 of updateAnnotation: validate and build the updated list.
- * Returns null if the update should be skipped (identical annotation).
+ * Pure: given the current annotations and a proposed updated annotation, plan
+ * the full update. Returns { kind: "noop" } if the update would be a no-op, or
+ * { kind: "update", newAnnotations, newDocumentText } describing what needs to
+ * be written.
+ *
+ * newDocumentText is non-null iff the updated annotation's document differs
+ * from the current on-disk document text.
  */
-export function buildAnnotationUpdate(
-  annotations: Annotation[],
-  updatedAnnotation: Annotation,
-  currentDocText: string
-): Annotation[] | null {
-  const fixedDoc = updatedAnnotation.document || currentDocText;
-  const existing = annotations.find((a) => a.id === updatedAnnotation.id);
-  if (existing && annotationsAreIdentical(existing, { ...updatedAnnotation, document: fixedDoc })) {
-    console.log("Skipping annotation update because it is identical to the existing annotation");
-    return null;
+export function planAnnotationUpdate(
+  currentAnnotations: Annotation[],
+  updatedAnnotation: AnnotationUpdate,
+  currentDocumentText: string
+): AnnotationUpdatePlan {
+  // TODO this isn't correctly handling mixed file writes between the user and the extension, it's very tricky
+  // fortunately we should be able to unit test to describe and validate the intended behavior
+  const currentAnnotation = currentAnnotations.find((a) => a.id === updatedAnnotation.id)!;
+  const resolvedDoc = updatedAnnotation.settingAnchorTextOnly ? currentDocumentText.slice(0, currentAnnotation.start) + updatedAnnotation.document.slice(updatedAnnotation.start, updatedAnnotation.end) + currentDocumentText.slice(currentAnnotation.end) : updatedAnnotation.document || currentDocumentText;
+  const normalized: AnnotationUpdate = { ...updatedAnnotation, document: resolvedDoc };
+
+  const existing = currentAnnotations.find((a) => a.id === updatedAnnotation.id);
+  if (existing && annotationsAreIdentical(existing, normalized)) {
+    return { kind: "noop" };
   }
-  return patchAnnotationInList(annotations, updatedAnnotation.id, updatedAnnotation, currentDocText);
+
+  const newAnnotations = currentAnnotations.map((a) =>
+    a.id === updatedAnnotation.id ? normalized : a
+  );
+
+  const newDocumentText = resolvedDoc !== currentDocumentText ? resolvedDoc : null;
+
+  return { kind: "update", newAnnotations, newDocumentText };
 }
 
 
 // ═══════════════════════════════════════════════════════════════════════════════
-// I/O functions — read/write disk and VS Code APIs. No TrackerState access.
-// (Unchanged from the original.)
+// Shell: I/O and VSCode API. These are the only functions allowed to touch the
+// filesystem, VSCode APIs, or the panel.
 // ═══════════════════════════════════════════════════════════════════════════════
 
 function readAnnotationsFromDisk(documentFsPath: string): Annotation[] | null {
@@ -335,70 +439,91 @@ function readAnnotationsFromDisk(documentFsPath: string): Annotation[] | null {
   }
 }
 
-function writeAnnotationsToDisk(
-  annotations: Annotation[],
-  document: vscode.TextDocument
-): void {
-  if (annotations.length === 0) {
-    return;
-  }
-  const annotationsUri = getAnnotationsFilePath(document.uri.fsPath, true);
-  const dir = path.dirname(annotationsUri);
-  if (!fs.existsSync(dir)) {
-    fs.mkdirSync(dir, { recursive: true });
+/**
+ * Synchronously write the annotation list for a document. An empty list deletes
+ * the annotations file. Returns true on success, false on failure.
+ */
+function tryWriteAnnotationsFile(
+  documentFsPath: string,
+  documentText: string,
+  fileName: string,
+  annotations: Annotation[]
+): boolean {
+  try {
+    const annotationsPath = getAnnotationsFilePath(documentFsPath, annotations.length > 0);
+
+    if (annotations.length === 0) {
+      if (fs.existsSync(annotationsPath)) {
+        fs.unlinkSync(annotationsPath);
+      }
+      return true;
+    }
+
+    const dir = path.dirname(annotationsPath);
+    if (!fs.existsSync(dir)) {
+      fs.mkdirSync(dir, { recursive: true });
+    }
+    const state = serializeAnnotationsForDisk(annotations, documentText, fileName);
+    fs.writeFileSync(annotationsPath, JSON.stringify(state, null, 2), "utf8");
+    console.debug(`Saved annotations to ${annotationsPath}`);
+    return true;
+  } catch (error) {
+    console.error(`Failed to write annotations for ${documentFsPath}:`, error);
+    return false;
   }
-  console.debug(`Saving annotations to ${annotationsUri}`);
-  const state = serializeAnnotationsForDisk(annotations, document.getText(), document.fileName);
-  fs.writeFileSync(annotationsUri, JSON.stringify(state, null, 2), "utf8");
 }
 
-function deleteAnnotationsFile(documentFsPath: string): void {
+/**
+ * Synchronously write new text to a document file on disk, bypassing VSCode's
+ * edit API entirely. The file watcher will eventually fire onchange; that's
+ * handled by the short-circuit in applyChangesToAnnotations.
+ */
+function tryWriteDocumentFile(documentFsPath: string, newText: string): boolean {
   try {
-    const filePath = getAnnotationsFilePath(documentFsPath);
-    if (fs.existsSync(filePath)) {
-      fs.unlinkSync(filePath);
-    }
+    fs.writeFileSync(documentFsPath, newText, "utf8");
+    return true;
   } catch (error) {
-    console.error("Failed to remove annotations file:", error);
+    console.error(`Failed to write document ${documentFsPath}:`, error);
+    return false;
   }
 }
 
-function notifyPanel(document: vscode.TextDocument, annotations: Annotation[]): void {
-  console.log("Notifying annotation panel of changes for document", document.uri.toString());
-  if (AnnotationManagerPanel.currentPanel) {
-    AnnotationManagerPanel.currentPanel.sendMessageObject({
-      command: "updateAnnotations",
-      data: {
-        documentUri: document.uri.toString(),
-        annotations,
-        documentText: document.getText(),
-      },
-    });
+function notifyPanel(
+  documentUri: vscode.Uri,
+  annotations: Annotation[],
+  documentText: string
+): void {
+  if (!AnnotationManagerPanel.currentPanel) {
+    return;
   }
+  console.log("Notifying annotation panel of changes for document", documentUri.toString());
+  AnnotationManagerPanel.currentPanel.sendMessageObject({
+    command: "updateAnnotations",
+    data: {
+      documentUri: documentUri.toString(),
+      annotations,
+      documentText,
+    },
+  });
 }
 
 /**
- * Disposes old decoration types for a document key, creates new ones from the
- * given annotations, applies them to visible editors, and returns the new
- * decoration type array.
+ * Execute a list of decoration specs: dispose old disposers, create new VSCode
+ * decoration types for each spec, apply them to visible editors of `document`,
+ * and return the new disposer list.
  */
-function rebuildDecorations(
-  oldDecorations: vscode.TextEditorDecorationType[] | undefined,
-  annotations: Annotation[],
+function applyDecorations(
+  oldDisposers: DecorationDisposer[] | undefined,
+  specs: DecorationSpec[],
   document: vscode.TextDocument
-): vscode.TextEditorDecorationType[] {
-  const documentKey = document.uri.toString();
-
-  console.log("Updating decorations for document", documentKey);
-  console.log(annotations);
-
-  // Dispose old
-  if (oldDecorations) {
-    for (const d of oldDecorations) {
-      d.dispose();
+): DecorationDisposer[] {
+  if (oldDisposers) {
+    for (const dispose of oldDisposers) {
+      try { dispose(); } catch (e) { console.error("Decoration dispose failed:", e); }
     }
   }
 
+  const documentKey = document.uri.toString();
   const editors = vscode.window.visibleTextEditors.filter(
     (e) => e.document.uri.toString() === documentKey
   );
@@ -406,31 +531,21 @@ function rebuildDecorations(
     return [];
   }
 
-  const selectedAnnotationId = AnnotationManagerPanel.currentPanel?.selectedAnnotationId;
-  const docText = document.getText();
-  const result: vscode.TextEditorDecorationType[] = [];
+  const disposers: DecorationDisposer[] = [];
 
-  for (const annotation of annotations) {
-    if (annotation.document !== docText) {
-      continue;
-    }
+  for (const spec of specs) {
     try {
-      const isSelected = selectedAnnotationId === annotation.id;
-      const baseColor = annotation.metadata?.color || "rgba(255,255,0,0.3)";
-      const decorationColor = resolveDecorationColor(baseColor, isSelected);
-      const gutterColor = resolveGutterColor(baseColor);
-
-      const startPos = document.positionAt(annotation.start);
-      const endPos = document.positionAt(annotation.end);
+      const startPos = document.positionAt(spec.startOffset);
+      const endPos = document.positionAt(spec.endOffset);
       const range = new vscode.Range(startPos, endPos);
 
       const textDecorationType = vscode.window.createTextEditorDecorationType({
-        borderColor: decorationColor,
+        borderColor: spec.textBorderColor,
         borderStyle: "none none solid none",
       });
       const gutterDecorationType = vscode.window.createTextEditorDecorationType({
         isWholeLine: true,
-        borderColor: gutterColor,
+        borderColor: spec.gutterBorderColor,
         borderWidth: "3px",
         borderStyle: "none solid none none",
       });
@@ -440,413 +555,350 @@ function rebuildDecorations(
         editor.setDecorations(gutterDecorationType, [range]);
       }
 
-      result.push(textDecorationType, gutterDecorationType);
+      disposers.push(() => textDecorationType.dispose());
+      disposers.push(() => gutterDecorationType.dispose());
     } catch (error) {
       console.error("Error creating decoration:", error);
     }
   }
 
-  return result;
-}
-
-async function applyAnnotationDocumentTextEdit(
-  document: vscode.TextDocument,
-  newText: string
-): Promise<boolean> {
-  const edit = new vscode.WorkspaceEdit();
-  const fullRange = new vscode.Range(
-    document.positionAt(0),
-    document.positionAt(document.getText().length)
-  );
-  edit.replace(document.uri, fullRange, newText);
-  return vscode.workspace.applyEdit(edit);
+  return disposers;
 }
 
 
 // ═══════════════════════════════════════════════════════════════════════════════
-// Immutable state helpers. Every transition returns a new TrackerState; Maps
-// are cloned, not mutated. Object.freeze is applied at the top level (Maps
-// themselves remain structurally mutable, so correctness relies on never
-// calling .set/.delete on them outside these helpers).
+// createAnnotationTracker — the only place that owns state. State construction
+// happens here and only here.
 // ═══════════════════════════════════════════════════════════════════════════════
 
-function mapWith<K, V>(m: ReadonlyMap<K, V>, key: K, value: V): ReadonlyMap<K, V> {
-  const next = new Map(m);
-  next.set(key, value);
-  return next;
-}
-
-function mapWithout<K, V>(m: ReadonlyMap<K, V>, key: K): ReadonlyMap<K, V> {
-  const next = new Map(m);
-  next.delete(key);
-  return next;
-}
-
-function withAnnotations(s: TrackerState, key: string, anns: Annotation[]): TrackerState {
-  return { ...s, documentAnnotations: mapWith(s.documentAnnotations, key, anns) };
-}
-function withDecorationTypes(s: TrackerState, key: string, types: vscode.TextEditorDecorationType[]): TrackerState {
-  return { ...s, oldDecorationCleanupFunctions: mapWith(s.oldDecorationCleanupFunctions, key, types) };
-}
-function withContentCache(s: TrackerState, key: string, text: string): TrackerState {
-  return { ...s, documentContentCache: mapWith(s.documentContentCache, key, text) };
-}
-function withPendingChanges(s: TrackerState, key: string, changes: vscode.TextDocumentContentChangeEvent[]): TrackerState {
-  return { ...s, pendingChanges: mapWith(s.pendingChanges, key, changes) };
-}
-function withoutPendingChanges(s: TrackerState, key: string): TrackerState {
-  return { ...s, pendingChanges: mapWithout(s.pendingChanges, key) };
-}
-function withTimer(s: TrackerState, key: string, timer: NodeJS.Timeout): TrackerState {
-  return { ...s, fileChangeTimers: mapWith(s.fileChangeTimers, key, timer) };
-}
-function withoutTimer(s: TrackerState, key: string): TrackerState {
-  return { ...s, fileChangeTimers: mapWithout(s.fileChangeTimers, key) };
+export interface TrackerHandle extends vscode.Disposable {
+  readonly state: Readonly<TrackerState>;
+  loadAnnotationsForDocument(document: vscode.TextDocument): Annotation[];
+  saveAnnotationsForDocument(document: vscode.TextDocument): void;
+  addAnnotation(document: vscode.TextDocument, annotation: Annotation): void;
+  removeAnnotation(document: vscode.TextDocument, annotationId: string): void;
+  updateAnnotation(document: vscode.TextDocument, updatedAnnotation: AnnotationUpdate): void;
+  moveAnnotation(
+    document: vscode.TextDocument,
+    annotationId: string,
+    newStart: number,
+    newEnd: number
+  ): void;
+  getAnnotationsForDocument(document: vscode.TextDocument): Annotation[];
+  updateDecorations(document: vscode.TextDocument): void;
+  dispose(): void;
 }
 
+export function createAnnotationTracker(_context: vscode.ExtensionContext): TrackerHandle {
+  let state: TrackerState = {
+    documentAnnotations: new Map(),
+    decorationDisposers: new Map(),
+    fileChangeTimers: new Map(),
+    pendingChanges: new Map(),
+  };
 
-// ═══════════════════════════════════════════════════════════════════════════════
-// State transitions. Each takes a TrackerState and returns a new TrackerState.
-// Side effects (disk I/O, editor decorations, panel notifications) may happen,
-// but in-memory state is only updated via the returned value.
-// ═══════════════════════════════════════════════════════════════════════════════
-
-function refreshDecorationsAndNotify(state: TrackerState, document: vscode.TextDocument): TrackerState {
-  const key = document.uri.toString();
-  const annotations = state.documentAnnotations.get(key) || [];
-  const oldTypes = state.oldDecorationCleanupFunctions.get(key);
-  const newTypes = rebuildDecorations(oldTypes, annotations, document);
-  notifyPanel(document, annotations);
-  return withDecorationTypes(state, key, newTypes);
-}
+  const getSelectedId = (): string | undefined =>
+    AnnotationManagerPanel.currentPanel?.selectedAnnotationId;
+
+  /**
+   * Top-level commit: given a document and a new annotation list, rebuild
+   * decorations against the document, update state, and notify the panel.
+   * This is the single place where decoration disposers and documentAnnotations
+   * are swapped together — it combines I/O (decoration API, panel message) with
+   * the resulting state update.
+   */
+  const commitAnnotations = (
+    document: vscode.TextDocument,
+    newAnnotations: Annotation[]
+  ): void => {
+    const key = document.uri.toString();
+    const specs = computeDecorationSpecs(newAnnotations, document.getText(), getSelectedId());
+    const newDisposers = applyDecorations(state.decorationDisposers.get(key), specs, document);
+
+    const nextAnnotations = new Map(state.documentAnnotations);
+    nextAnnotations.set(key, newAnnotations);
+    const nextDisposers = new Map(state.decorationDisposers);
+    nextDisposers.set(key, newDisposers);
+
+    state = {
+      documentAnnotations: nextAnnotations,
+      decorationDisposers: nextDisposers,
+      fileChangeTimers: state.fileChangeTimers,
+      pendingChanges: state.pendingChanges,
+    };
 
-function saveAndRefresh(state: TrackerState, document: vscode.TextDocument): TrackerState {
-  const annotations = state.documentAnnotations.get(document.uri.toString()) || [];
-  writeAnnotationsToDisk(annotations, document);
-  return refreshDecorationsAndNotify(state, document);
-}
+    notifyPanel(document.uri, newAnnotations, document.getText());
+  };
 
-function loadAnnotationsForDocument(state: TrackerState, document: vscode.TextDocument): TrackerState {
-  const key = document.uri.toString();
-  console.debug(`Loading annotations for ${key}`);
-  // TODO we have only sort-of validated that diff loading works correctly.
-  if (state.documentAnnotations.has(key)) {
-    return state;
-  }
-  const loaded = readAnnotationsFromDisk(document.uri.fsPath);
-  if (loaded !== null) {
-    return refreshDecorationsAndNotify(withAnnotations(state, key, loaded), document);
-  }
+  /** Load annotations for a document if not already loaded. */
+  const ensureLoaded = (document: vscode.TextDocument): void => {
+    const key = document.uri.toString();
+    if (state.documentAnnotations.has(key)) {
+      return;
+    }
+    const loaded = readAnnotationsFromDisk(document.uri.fsPath);
+    if (loaded !== null) {
+      commitAnnotations(document, loaded);
+      return;
+    }
+    // No file on disk — record an empty entry without notifying the panel,
+    // matching the original behavior.
+    const nextAnnotations = new Map(state.documentAnnotations);
+    nextAnnotations.set(key, []);
+    state = {
+      documentAnnotations: nextAnnotations,
+      decorationDisposers: state.decorationDisposers,
+      fileChangeTimers: state.fileChangeTimers,
+      pendingChanges: state.pendingChanges,
+    };
+  };
 
-  return withAnnotations(state, key, []);
-}
+  /** Flush accumulated pending changes for a document key. */
+  const flushPendingChanges = (documentKey: string): void => {
+    const editor = vscode.window.activeTextEditor;
+    if (!editor || editor.document.uri.toString() !== documentKey) {
+      console.error(
+        "Editor not active or document not loaded",
+        editor?.document.uri.toString(),
+        documentKey
+      );
+      const clearedPending = new Map(state.pendingChanges);
+      clearedPending.delete(documentKey);
+      const clearedTimers = new Map(state.fileChangeTimers);
+      clearedTimers.delete(documentKey);
+      state = {
+        documentAnnotations: state.documentAnnotations,
+        decorationDisposers: state.decorationDisposers,
+        fileChangeTimers: clearedTimers,
+        pendingChanges: clearedPending,
+      };
+      return;
+    }
 
-function getAnnotationsForDocument(state: TrackerState, document: vscode.TextDocument): Annotation[] {
-  return state.documentAnnotations.get(document.uri.toString()) || [];
-}
+    const document = editor.document;
+    const annotations = state.documentAnnotations.get(documentKey);
+    const changes = state.pendingChanges.get(documentKey) || [];
+
+    // Clear the pending/timer entries regardless of whether we have work to do.
+    const clearedPending = new Map(state.pendingChanges);
+    clearedPending.delete(documentKey);
+    const clearedTimers = new Map(state.fileChangeTimers);
+    clearedTimers.delete(documentKey);
+    state = {
+      documentAnnotations: state.documentAnnotations,
+      decorationDisposers: state.decorationDisposers,
+      fileChangeTimers: clearedTimers,
+      pendingChanges: clearedPending,
+    };
 
-function processAccumulatedChanges(state: TrackerState, document: vscode.TextDocument): TrackerState {
-  const key = document.uri.toString();
-  const annotations = state.documentAnnotations.get(key);
-  const changes = state.pendingChanges.get(key) || [];
-  if (!annotations || annotations.length === 0 || changes.length === 0) {
-    return state;
-  }
-  const startingContent = annotations[0].document;
-  const currentContent = document.getText();
-  const updated = applyChangesToAnnotations(annotations, changes, startingContent, currentContent);
-  return saveAndRefresh(withAnnotations(state, key, updated), document);
-}
+    if (!annotations || annotations.length === 0 || changes.length === 0) {
+      return;
+    }
 
-/**
- * Triggered by the deferred flush timer. Processes whatever changes have
- * accumulated for `documentKey`, re-seeds the content cache, and clears the
- * pending-changes / timer entries.
- */
-function flushAccumulatedChanges(state: TrackerState, documentKey: string): TrackerState {
-  const editor = vscode.window.activeTextEditor;
-  if (!editor || editor.document.uri.toString() !== documentKey) {
-    console.error(
-      "Editor not active or document not loaded",
-      editor,
-      editor?.document.uri.toString(),
-      documentKey
+    const startingContent = annotations[0].document;
+    const currentContent = document.getText();
+    const updated = applyChangesToAnnotations(annotations, changes, startingContent, currentContent);
+
+    // Persist the (possibly-unchanged) annotations and unconditionally rebuild
+    // decorations. The unconditional rebuild matters: if updateAnnotation just
+    // rewrote the document on disk, VSCode will fire onchange with a no-op
+    // applyChangesToAnnotations result — but decorations still need to be
+    // rebuilt against the refreshed document text.
+    tryWriteAnnotationsFile(
+      document.uri.fsPath,
+      document.getText(),
+      document.fileName,
+      updated
     );
-    return withoutTimer(withoutPendingChanges(state, documentKey), documentKey);
-  }
-  const afterProcess = processAccumulatedChanges(state, editor.document);
-  const afterCache = withContentCache(afterProcess, documentKey, editor.document.getText());
-  return withoutTimer(withoutPendingChanges(afterCache, documentKey), documentKey);
-}
-
-/**
- * `scheduleFlush` is a narrow capability: it only lets the callee arrange for
- * a known future transition (flushAccumulatedChanges) to run on docKey. It
- * does NOT expose setState. The existing timer is cleared here because
- * clearTimeout is a side effect on the OS, not a state mutation.
- */
-function onDocumentChanged(
-  state: TrackerState,
-  event: vscode.TextDocumentChangeEvent,
-  scheduleFlush: (documentKey: string) => NodeJS.Timeout
-): TrackerState {
-  const docKey = event.document.uri.toString();
-
-  if (!state.documentAnnotations.has(docKey)) {
-    return state;
-  }
-
-  if (!state.documentContentCache.has(docKey)) {
-    return withContentCache(state, docKey, event.document.getText());
-  }
-
-  const existingChanges = state.pendingChanges.get(docKey) || [];
-  const nextChanges = [...existingChanges, ...event.contentChanges];
-
-  const existingTimer = state.fileChangeTimers.get(docKey);
-  if (existingTimer) {
-    clearTimeout(existingTimer);
-  }
-  const newTimer = scheduleFlush(docKey);
-
-  return withTimer(withPendingChanges(state, docKey, nextChanges), docKey, newTimer);
-}
-
-function onActiveEditorChanged(
-  state: TrackerState,
-  editor: vscode.TextEditor | undefined
-): TrackerState {
-  if (!editor) {
-    return state;
-  }
-  const afterLoad = loadAnnotationsForDocument(state, editor.document);
-  return withContentCache(afterLoad, editor.document.uri.toString(), editor.document.getText());
-}
-
-function addAnnotation(
-  state: TrackerState,
-  document: vscode.TextDocument,
-  annotation: Annotation
-): TrackerState {
-  const key = document.uri.toString();
-  const annotations = state.documentAnnotations.get(key) || [];
-  return saveAndRefresh(withAnnotations(state, key, [...annotations, annotation]), document);
-}
-
-function removeAnnotation(
-  state: TrackerState,
-  document: vscode.TextDocument,
-  annotationId: string
-): TrackerState {
-  const key = document.uri.toString();
-  const annotations = state.documentAnnotations.get(key) || [];
-  const updated = annotations.filter((a) => a.id !== annotationId);
-  const next = withAnnotations(state, key, updated);
-  if (updated.length === 0) {
-    deleteAnnotationsFile(document.uri.fsPath);
-    return refreshDecorationsAndNotify(next, document);
-  }
-  return saveAndRefresh(next, document);
-}
-
-function moveAnnotation(
-  state: TrackerState,
-  document: vscode.TextDocument,
-  annotationId: string,
-  newStart: number,
-  newEnd: number
-): TrackerState {
-  const key = document.uri.toString();
-  const annotations = state.documentAnnotations.get(key) || [];
-  const index = annotations.findIndex((a) => a.id === annotationId);
-  if (index === -1) {
-    vscode.window.showErrorMessage(`Annotation with ID ${annotationId} not found.`);
-    return state;
-  }
-  const updated = annotations.map((a, i) =>
-    i === index ? { ...a, start: newStart, end: newEnd, document: document.getText() } : a
-  );
-  return saveAndRefresh(withAnnotations(state, key, updated), document);
-}
-
-
-// ─── updateAnnotation phases ──────────────────────────────────────────────────
-// updateAnnotation has an async workspace-edit step that may race with other
-// events. To preserve the original's "re-read state after each await" behavior
-// without leaking getState/setState into the helper, the async orchestration
-// lives in the returned method of createAnnotationTracker; each phase below is
-// a pure state transition invoked between awaits.
-
-interface UpdateBeginResult {
-  nextState: TrackerState;
-  needsDocumentEdit: boolean;
-  skipped: boolean;
-}
-
-function beginAnnotationUpdate(
-  state: TrackerState,
-  document: vscode.TextDocument,
-  updatedAnnotation: Annotation
-): UpdateBeginResult {
-  console.log(
-    "Updating annotation", updatedAnnotation.id,
-    "for document", document.uri.toString(),
-    "with updated annotation", updatedAnnotation
-  );
-  const key = document.uri.toString();
-  const annotations = state.documentAnnotations.get(key) || [];
-  const updated = buildAnnotationUpdate(annotations, updatedAnnotation, document.getText());
-  if (updated === null) {
-    return { nextState: state, needsDocumentEdit: false, skipped: true };
-  }
-  writeAnnotationsToDisk(updated, document);
-  const needsDocumentEdit =
-    !!updatedAnnotation.document && updatedAnnotation.document !== document.getText();
-  return {
-    nextState: withAnnotations(state, key, updated),
-    needsDocumentEdit,
-    skipped: false,
+    commitAnnotations(document, updated);
   };
-}
 
-function completeAnnotationUpdateAfterEdit(
-  state: TrackerState,
-  document: vscode.TextDocument,
-  updatedAnnotation: Annotation
-): TrackerState {
-  const key = document.uri.toString();
-  const annotations = state.documentAnnotations.get(key) || [];
-  const repatched = patchAnnotationInList(
-    annotations,
-    updatedAnnotation.id,
-    updatedAnnotation,
-    document.getText()
-  );
-  return saveAndRefresh(withAnnotations(state, key, repatched), document);
-}
-
-function revertAnnotationUpdate(
-  state: TrackerState,
-  document: vscode.TextDocument,
-  updatedAnnotation: Annotation
-): TrackerState {
-  console.error("Failed to update document text to match annotation");
-  const key = document.uri.toString();
-  const annotations = state.documentAnnotations.get(key) || [];
-  const reverted = annotations.map((a) =>
-    a.id === updatedAnnotation.id ? { ...a, document: document.getText() } : a
-  );
-  return refreshDecorationsAndNotify(withAnnotations(state, key, reverted), document);
-}
+  /** Handle a VSCode text-document change event. */
+  const onDocumentChanged = (event: vscode.TextDocumentChangeEvent): void => {
+    const docKey = event.document.uri.toString();
+    if (!state.documentAnnotations.has(docKey)) {
+      return;
+    }
 
+    const parsed = event.contentChanges.map(parseContentChange);
+    const existingChanges = state.pendingChanges.get(docKey) || [];
+    const nextChanges = [...existingChanges, ...parsed];
 
-// ═══════════════════════════════════════════════════════════════════════════════
-// createAnnotationTracker — the only place that owns state.
-// ═══════════════════════════════════════════════════════════════════════════════
-
-export interface TrackerHandle extends vscode.Disposable {
-  readonly state: Readonly<TrackerState>;
-  loadAnnotationsForDocument(document: vscode.TextDocument): Promise<Annotation[]>;
-  saveAnnotationsForDocument(document: vscode.TextDocument): Promise<void>;
-  addAnnotation(document: vscode.TextDocument, annotation: Annotation): void;
-  removeAnnotation(document: vscode.TextDocument, annotationId: string): void;
-  updateAnnotation(document: vscode.TextDocument, updatedAnnotation: Annotation): Promise<void>;
-  moveAnnotation(document: vscode.TextDocument, annotationId: string, newStart: number, newEnd: number): void;
-  getAnnotationsForDocument(document: vscode.TextDocument): Annotation[];
-  updateDecorations(document: vscode.TextDocument): void;
-  dispose(): void;
-}
+    const existingTimer = state.fileChangeTimers.get(docKey);
+    if (existingTimer) {
+      clearTimeout(existingTimer);
+    }
+    const newTimer = setTimeout(() => flushPendingChanges(docKey), 50);
+
+    const nextPending = new Map(state.pendingChanges);
+    nextPending.set(docKey, nextChanges);
+    const nextTimers = new Map(state.fileChangeTimers);
+    nextTimers.set(docKey, newTimer);
+
+    state = {
+      documentAnnotations: state.documentAnnotations,
+      decorationDisposers: state.decorationDisposers,
+      fileChangeTimers: nextTimers,
+      pendingChanges: nextPending,
+    };
+  };
 
-export function createAnnotationTracker(_context: vscode.ExtensionContext): TrackerHandle {
-  let state: Readonly<TrackerState> = {
-    documentAnnotations: new Map(),
-    oldDecorationCleanupFunctions: new Map(),
-    fileChangeTimers: new Map(),
-    documentContentCache: new Map(),
-    pendingChanges: new Map(),
+  /** Handle a VSCode active-editor change event. */
+  const onActiveEditorChanged = (editor: vscode.TextEditor | undefined): void => {
+    if (!editor) {
+      return;
+    }
+    ensureLoaded(editor.document);
   };
 
-  const getState = (): TrackerState => state;
-  const setState = (next: TrackerState): void => { state = next; };
-
-  // Narrow capability handed to onDocumentChanged. Not setState — only the
-  // ability to schedule a known future transition on a known docKey.
-  const scheduleFlush = (docKey: string): NodeJS.Timeout =>
-    setTimeout(() => setState(flushAccumulatedChanges(getState(), docKey)), 50);
-
-  const disposables = [
-    vscode.workspace.onDidChangeTextDocument((e) =>
-      setState(onDocumentChanged(getState(), e, scheduleFlush))
-    ),
-    vscode.window.onDidChangeActiveTextEditor((editor) =>
-      setState(onActiveEditorChanged(getState(), editor))
-    ),
+  const disposables: vscode.Disposable[] = [
+    vscode.workspace.onDidChangeTextDocument(onDocumentChanged),
+    vscode.window.onDidChangeActiveTextEditor(onActiveEditorChanged),
   ];
 
-  // Initial load. No conditional here — onActiveEditorChanged handles the
-  // undefined-editor case internally.
-  setState(onActiveEditorChanged(getState(), vscode.window.activeTextEditor));
+  // Initial load. onActiveEditorChanged handles the undefined case internally.
+  onActiveEditorChanged(vscode.window.activeTextEditor);
 
   return {
-    get state() { return getState(); },
+    get state() { return state; },
 
-    loadAnnotationsForDocument: async (doc) => {
-      setState(loadAnnotationsForDocument(getState(), doc));
-      return getAnnotationsForDocument(getState(), doc);
+    loadAnnotationsForDocument(document) {
+      ensureLoaded(document);
+      return state.documentAnnotations.get(document.uri.toString()) || [];
     },
 
-    saveAnnotationsForDocument: async (doc) => {
-      writeAnnotationsToDisk(getAnnotationsForDocument(getState(), doc), doc);
+    saveAnnotationsForDocument(document) {
+      const annotations = state.documentAnnotations.get(document.uri.toString()) || [];
+      tryWriteAnnotationsFile(
+        document.uri.fsPath,
+        document.getText(),
+        document.fileName,
+        annotations
+      );
     },
 
-    addAnnotation: (doc, ann) => setState(addAnnotation(getState(), doc, ann)),
-
-    removeAnnotation: (doc, id) => setState(removeAnnotation(getState(), doc, id)),
+    addAnnotation(document, annotation) {
+      const key = document.uri.toString();
+      const current = state.documentAnnotations.get(key) || [];
+      const newAnnotations = [...current, annotation];
+      tryWriteAnnotationsFile(
+        document.uri.fsPath,
+        document.getText(),
+        document.fileName,
+        newAnnotations
+      );
+      commitAnnotations(document, newAnnotations);
+    },
 
-    updateAnnotation: async (doc, ann) => {
-      // Phase 1: sync validate + patch + write.
-      const { nextState, needsDocumentEdit, skipped } = beginAnnotationUpdate(getState(), doc, ann);
-      if (skipped) { return; }
-      setState(nextState);
+    removeAnnotation(document, annotationId) {
+      const key = document.uri.toString();
+      const current = state.documentAnnotations.get(key) || [];
+      const newAnnotations = current.filter((a) => a.id !== annotationId);
+      tryWriteAnnotationsFile(
+        document.uri.fsPath,
+        document.getText(),
+        document.fileName,
+        newAnnotations
+      );
+      commitAnnotations(document, newAnnotations);
+    },
 
-      // Phase 2a: no workspace edit required — just refresh decorations.
-      if (!needsDocumentEdit) {
-        setState(refreshDecorationsAndNotify(getState(), doc));
-        console.debug("Finished updating annotation", ann);
+    /**
+     * The centerpiece: fully synchronous update.
+     *
+     *   1. Plan the update (pure).
+     *   2. If no-op, return.
+     *   3. SYNC write annotations. On failure, return old state.
+     *   4. If the document text changed, SYNC write the document. On failure,
+     *      SYNC revert the annotations file and return old state.
+     *   5. Commit: rebuild decorations, update state, notify panel.
+     *
+     * The subsequent onchange from VSCode's file watcher is benign: the
+     * annotations already reflect the new text, so applyChangesToAnnotations
+     * short-circuits on startingContent === currentContent.
+     */
+    updateAnnotation(document, updatedAnnotation) {
+      const key = document.uri.toString();
+      const currentAnnotations = state.documentAnnotations.get(key) || [];
+      const plan = planAnnotationUpdate(currentAnnotations, updatedAnnotation, document.getText());
+
+      if (plan.kind === "noop") {
+        console.log("Skipping annotation update; identical to existing annotation");
         return;
       }
 
-      // Phase 2b: apply workspace edit. Each await re-reads state afterwards
-      // via getState() so we survive concurrent mutations.
-      console.debug("Annotation document text differs from current; applying workspace edit");
-      const success = await applyAnnotationDocumentTextEdit(doc, ann.document);
-      if (!success) {
-        setState(revertAnnotationUpdate(getState(), doc, ann));
+      // Effect 1: write the new annotation list.
+      const wroteAnnotations = tryWriteAnnotationsFile(
+        document.uri.fsPath,
+        document.getText(),
+        document.fileName,
+        plan.newAnnotations
+      );
+      if (!wroteAnnotations) {
         return;
       }
 
-      setState(completeAnnotationUpdateAfterEdit(getState(), doc, ann));
-
-      // Re-open the document to pick up any normalization vscode may have done
-      // (line endings, etc.) and patch one more time against that canonical text.
-      const updatedDoc = await vscode.workspace.openTextDocument(doc.uri);
-      setState(completeAnnotationUpdateAfterEdit(getState(), updatedDoc, ann));
+      // Effect 2 (conditional): write the new document text.
+      if (plan.newDocumentText !== null) {
+        const wroteDoc = tryWriteDocumentFile(document.uri.fsPath, plan.newDocumentText);
+        if (!wroteDoc) {
+          // Revert: put the old annotation list back. This "should (mostly)
+          // always succeed since we just wrote to it".
+          tryWriteAnnotationsFile(
+            document.uri.fsPath,
+            document.getText(),
+            document.fileName,
+            currentAnnotations
+          );
+          return;
+        }
+      }
 
-      console.debug("Finished updating annotation", ann);
+      // Commit decorations + state + panel. Note: VSCode's in-memory document
+      // may still hold the OLD text at this moment; decoration positions will
+      // briefly be computed against it. The file-watcher onchange will fire
+      // shortly after and flushPendingChanges will rebuild decorations against
+      // the refreshed document.
+      commitAnnotations(document, plan.newAnnotations);
     },
 
-    moveAnnotation: (doc, id, start, end) => setState(moveAnnotation(getState(), doc, id, start, end)),
+    moveAnnotation(document, annotationId, newStart, newEnd) {
+      const key = document.uri.toString();
+      const current = state.documentAnnotations.get(key) || [];
+      if (!current.some((a) => a.id === annotationId)) {
+        vscode.window.showErrorMessage(`Annotation with ID ${annotationId} not found.`);
+        return;
+      }
+      const newAnnotations = current.map((a) =>
+        a.id === annotationId
+          ? { ...a, start: newStart, end: newEnd, document: document.getText() }
+          : a
+      );
+      tryWriteAnnotationsFile(
+        document.uri.fsPath,
+        document.getText(),
+        document.fileName,
+        newAnnotations
+      );
+      commitAnnotations(document, newAnnotations);
+    },
 
-    getAnnotationsForDocument: (doc) => getAnnotationsForDocument(getState(), doc),
+    getAnnotationsForDocument(document) {
+      return state.documentAnnotations.get(document.uri.toString()) || [];
+    },
 
-    updateDecorations: (doc) => setState(refreshDecorationsAndNotify(getState(), doc)),
+    updateDecorations(document) {
+      const current = state.documentAnnotations.get(document.uri.toString()) || [];
+      commitAnnotations(document, current);
+    },
 
     dispose() {
-      const finalState = getState();
-      for (const types of finalState.oldDecorationCleanupFunctions.values()) {
-        for (const t of types) { t.dispose(); }
+      for (const disposers of state.decorationDisposers.values()) {
+        for (const d of disposers) {
+          try { d(); } catch (e) { console.error("Decoration dispose failed:", e); }
+        }
       }
-      for (const timer of finalState.fileChangeTimers.values()) {
+      for (const timer of state.fileChangeTimers.values()) {
         clearTimeout(timer);
       }
       for (const d of disposables) { d.dispose(); }

From 95965a107f14ccc29f3317af3ddcae060fcfd17c Mon Sep 17 00:00:00 2001
From: Edward Misback <misback@cs.washington.edu>
Date: Thu, 16 Apr 2026 07:03:23 -0400
Subject: [PATCH 20/22] Trying synchronous updates for now.

---
 vscode-extension/webview-ui/src/App.tsx | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/vscode-extension/webview-ui/src/App.tsx b/vscode-extension/webview-ui/src/App.tsx
index cc801fe..516cde9 100644
--- a/vscode-extension/webview-ui/src/App.tsx
+++ b/vscode-extension/webview-ui/src/App.tsx
@@ -8,6 +8,7 @@ interface AnnotationUpdate {
   end?: number;
   document?: string;
   metadata?: any;
+  settingAnchorTextOnly?: boolean;
 }
 
 export interface AnnotationEditorProps {
@@ -40,7 +41,7 @@ function AnnotationEditorContainer(props: {
       {toolTypes[value.tool]?.({
         value,
         setValue: (v: AnnotationUpdate) =>
-          setValue({ ...value, document: v.document, metadata: v.metadata }),
+          setValue({ ...value, document: v.document, metadata: v.metadata, settingAnchorTextOnly: v.settingAnchorTextOnly }),
         utils: {
           getText: () => value.document.slice(value.start, value.end),
           setText: (newText: string) => {
@@ -49,6 +50,7 @@ function AnnotationEditorContainer(props: {
               document:
                 value.document.slice(0, value.start) + newText + value.document.slice(value.end),
               metadata: value.metadata,
+              settingAnchorTextOnly: true 
             });
           },
           setMetadata: (newMetadata: any) => {

From d526244e5eff2b130137a74e963d2400f4010c96 Mon Sep 17 00:00:00 2001
From: Edward Misback <misback@cs.washington.edu>
Date: Thu, 16 Apr 2026 07:17:17 -0400
Subject: [PATCH 21/22] Bit more cleaning.

---
 vscode-extension/src/AnnotationTracker.ts | 35 ++++++++++++++++-------
 1 file changed, 24 insertions(+), 11 deletions(-)

diff --git a/vscode-extension/src/AnnotationTracker.ts b/vscode-extension/src/AnnotationTracker.ts
index fead001..b24303c 100644
--- a/vscode-extension/src/AnnotationTracker.ts
+++ b/vscode-extension/src/AnnotationTracker.ts
@@ -38,6 +38,19 @@ import * as fs from "fs";
 import { createPatch, applyPatch } from "diff";
 import { AnnotationManagerPanel } from "./panels/AnnotationManagerPanel";
 
+export const exportedForTesting = {
+  getAnnotationsFilePath,
+  reconstructAnnotationsFromDisk,
+  serializeAnnotationsForDisk,
+  parseContentChange,
+  applyChangeToAnnotation,
+  applyChangesToAnnotations,
+  resolveDecorationColor,
+  resolveGutterColor,
+  annotationsAreIdentical,
+  computeDecorationSpecs,
+  planAnnotationUpdate,
+};
 
 // ═══════════════════════════════════════════════════════════════════════════════
 // Domain types.
@@ -111,7 +124,7 @@ export type AnnotationUpdatePlan =
 // Pure functions — exported for testing. No I/O, no VSCode API, no TrackerState.
 // ═══════════════════════════════════════════════════════════════════════════════
 
-export function getAnnotationsFilePath(documentPath: string, createDir: boolean = false): string {
+function getAnnotationsFilePath(documentPath: string, createDir: boolean = false): string {
   let currentDir = path.dirname(documentPath);
 
   while (currentDir !== path.parse(currentDir).root) {
@@ -131,7 +144,7 @@ export function getAnnotationsFilePath(documentPath: string, createDir: boolean
   return path.join(annotationsDir, path.basename(documentPath) + ".annotations.json");
 }
 
-export function reconstructAnnotationsFromDisk(diskState: {
+function reconstructAnnotationsFromDisk(diskState: {
   document: string;
   annotations: (Annotation & { documentDiff?: string })[];
 }): Annotation[] {
@@ -152,7 +165,7 @@ export function reconstructAnnotationsFromDisk(diskState: {
   });
 }
 
-export function serializeAnnotationsForDisk(
+function serializeAnnotationsForDisk(
   annotations: Annotation[],
   documentText: string,
   fileName: string
@@ -197,7 +210,7 @@ export function serializeAnnotationsForDisk(
 }
 
 /** Anti-corruption: parse a VSCode change event into our domain type. */
-export function parseContentChange(event: vscode.TextDocumentContentChangeEvent): ContentChange {
+function parseContentChange(event: vscode.TextDocumentContentChangeEvent): ContentChange {
   return {
     rangeOffset: event.rangeOffset,
     rangeLength: event.rangeLength,
@@ -210,7 +223,7 @@ export function parseContentChange(event: vscode.TextDocumentContentChangeEvent)
  * isolation. Annotations whose document doesn't match the starting content are
  * passed through unchanged.
  */
-export function applyChangeToAnnotation(
+function applyChangeToAnnotation(
   annotation: Annotation,
   change: ContentChange,
   startingContent: string
@@ -294,7 +307,7 @@ export function applyChangeToAnnotation(
   return annotation;
 }
 
-export function applyChangesToAnnotations(
+function applyChangesToAnnotations(
   annotations: Annotation[],
   changes: readonly ContentChange[],
   startingContent: string,
@@ -317,7 +330,7 @@ export function applyChangesToAnnotations(
   );
 }
 
-export function resolveDecorationColor(baseColor: string, isSelected: boolean): string {
+function resolveDecorationColor(baseColor: string, isSelected: boolean): string {
   if (!isSelected) {
     return baseColor;
   }
@@ -337,7 +350,7 @@ export function resolveDecorationColor(baseColor: string, isSelected: boolean):
   return baseColor;
 }
 
-export function resolveGutterColor(baseColor: string): string {
+function resolveGutterColor(baseColor: string): string {
   if (baseColor.startsWith("rgba")) {
     const m = baseColor.match(/rgba\((\d+),\s*(\d+),\s*(\d+),\s*([\d.]+)\)/);
     if (m) { return `rgb(${m[1]}, ${m[2]}, ${m[3]})`; }
@@ -345,7 +358,7 @@ export function resolveGutterColor(baseColor: string): string {
   return baseColor;
 }
 
-export function annotationsAreIdentical(a: Annotation, b: Annotation): boolean {
+function annotationsAreIdentical(a: Annotation, b: Annotation): boolean {
   return (
     a.start === b.start &&
     a.end === b.end &&
@@ -358,7 +371,7 @@ export function annotationsAreIdentical(a: Annotation, b: Annotation): boolean {
  * Pure: compute the decoration specs for a list of annotations against a given
  * document text. Annotations whose document doesn't match are skipped.
  */
-export function computeDecorationSpecs(
+function computeDecorationSpecs(
   annotations: Annotation[],
   documentText: string,
   selectedAnnotationId: string | undefined
@@ -390,7 +403,7 @@ export function computeDecorationSpecs(
  * newDocumentText is non-null iff the updated annotation's document differs
  * from the current on-disk document text.
  */
-export function planAnnotationUpdate(
+function planAnnotationUpdate(
   currentAnnotations: Annotation[],
   updatedAnnotation: AnnotationUpdate,
   currentDocumentText: string

From f2f2fb4d1414da9a8c2504740ae8ae5464028156 Mon Sep 17 00:00:00 2001
From: Edward Misback <misback@cs.washington.edu>
Date: Thu, 16 Apr 2026 07:53:22 -0400
Subject: [PATCH 22/22] Add initial tests for AnnotationTracker.

---
 vscode-extension/package.json                 |   1 +
 vscode-extension/src/AnnotationTracker.ts     |  12 +-
 .../src/test/AnnotationTracker.test.ts        | 241 ++++++++++++++++++
 3 files changed, 251 insertions(+), 3 deletions(-)
 create mode 100644 vscode-extension/src/test/AnnotationTracker.test.ts

diff --git a/vscode-extension/package.json b/vscode-extension/package.json
index ac07a51..254a7db 100644
--- a/vscode-extension/package.json
+++ b/vscode-extension/package.json
@@ -87,6 +87,7 @@
     "compile": "tsc -p ./",
     "watch": "tsc -watch -p ./",
     "pretest": "npm run compile && npm run lint",
+    "test": "node --test out/test/AnnotationTracker.test.js",
     "lint": "eslint src --ext ts"
   },
   "devDependencies": {
diff --git a/vscode-extension/src/AnnotationTracker.ts b/vscode-extension/src/AnnotationTracker.ts
index b24303c..b8ef4cc 100644
--- a/vscode-extension/src/AnnotationTracker.ts
+++ b/vscode-extension/src/AnnotationTracker.ts
@@ -79,9 +79,15 @@ type AnnotationUpdate = Annotation & {
 
 /** Anti-corruption: parsed form of vscode.TextDocumentContentChangeEvent. */
 export interface ContentChange {
-  readonly rangeOffset: number;
-  readonly rangeLength: number;
-  readonly text: string;
+
+  /** number of characters from the start of the document */ 
+  readonly rangeOffset: number; 
+
+  /** number of characters replaced by this change */
+  readonly rangeLength: number; 
+
+  /** new text for this range */
+  readonly text: string; 
 }
 
 /** Anti-corruption: a DecorationType collapsed down to just the capability we use. */
diff --git a/vscode-extension/src/test/AnnotationTracker.test.ts b/vscode-extension/src/test/AnnotationTracker.test.ts
new file mode 100644
index 0000000..7a21940
--- /dev/null
+++ b/vscode-extension/src/test/AnnotationTracker.test.ts
@@ -0,0 +1,241 @@
+import assert from "assert/strict";
+import { test } from "node:test";
+
+import type { Annotation } from "../AnnotationTracker";
+
+const moduleLoader = require("module") as {
+  _load: (request: string, parent: NodeModule, isMain: boolean) => unknown;
+};
+
+const originalLoad = moduleLoader._load;
+const vscodeStub = {};
+
+moduleLoader._load = function patchedLoad(request: string, parent: NodeModule, isMain: boolean) {
+  if (request === "vscode") {
+    return vscodeStub;
+  }
+  return originalLoad(request, parent, isMain);
+};
+
+const { exportedForTesting } = require("../AnnotationTracker") as typeof import("../AnnotationTracker");
+
+moduleLoader._load = originalLoad;
+
+const { applyChangeToAnnotation } = exportedForTesting;
+
+function makeAnnotation(overrides: Partial<Annotation> = {}): Annotation {
+  const baseOriginal = {
+    document: "abcdefghi",
+    start: 4,
+    end: 10,
+  };
+
+  return {
+    id: "annotation-1",
+    start: 4,
+    end: 10,
+    document: "abcdefghi",
+    tool: "tool",
+    metadata: {},
+    ...overrides,
+    original: {
+      document: overrides.original?.document ?? baseOriginal.document,
+      start: overrides.original?.start ?? baseOriginal.start,
+      end: overrides.original?.end ?? baseOriginal.end,
+    },
+  };
+}
+
+test("returns the original annotation when the document does not match the starting content", () => {
+  const annotation = makeAnnotation({ document: "other-doc" });
+  const result = applyChangeToAnnotation(
+    annotation,
+    { rangeOffset: 0, rangeLength: 0, text: "x" },
+    "abcdefghi"
+  );
+
+  assert.strictEqual(result, annotation);
+});
+
+test("case 1: shifts the annotation when the change is completely before it", () => {
+  const annotation = makeAnnotation();
+  const result = applyChangeToAnnotation(
+    annotation,
+    { rangeOffset: 1, rangeLength: 1, text: "xy" },
+    "abcdefghi"
+  );
+
+  assert.deepStrictEqual(result, {
+    ...annotation,
+    start: 5,
+    end: 11,
+  });
+});
+
+test("case 2: leaves the annotation unchanged when the change is completely after it", () => {
+  const annotation = makeAnnotation();
+  const result = applyChangeToAnnotation(
+    annotation,
+    { rangeOffset: 12, rangeLength: 1, text: "xy" },
+    "abcdefghi"
+  );
+
+  assert.strictEqual(result, annotation);
+});
+
+test("case 3: updates the annotation when the change is immediately before it", () => {
+  const annotation = makeAnnotation();
+  const result = applyChangeToAnnotation(
+    annotation,
+    { rangeOffset: 2, rangeLength: 2, text: "XYZ" },
+    "abcdefghi"
+  );
+
+  assert.deepStrictEqual(result, {
+    ...annotation,
+    start: 2,
+    end: 11,
+  });
+});
+
+test("case 3 whitespace branch: shifts the annotation when whitespace is inserted immediately before it", () => {
+  const annotation = makeAnnotation();
+  const result = applyChangeToAnnotation(
+    annotation,
+    { rangeOffset: 3, rangeLength: 1, text: "  " },
+    "abcdefghi"
+  );
+
+  assert.deepStrictEqual(result, {
+    ...annotation,
+    start: 5,
+    end: 11,
+  });
+});
+
+test("case 4: extends the annotation when the change is immediately after it", () => {
+  const annotation = makeAnnotation();
+  const result = applyChangeToAnnotation(
+    annotation,
+    { rangeOffset: 10, rangeLength: 1, text: "XYZ" },
+    "abcdefghi"
+  );
+
+  assert.deepStrictEqual(result, {
+    ...annotation,
+    end: 13,
+  });
+});
+
+test("case 4 whitespace branch: leaves the annotation unchanged when whitespace is inserted immediately after it", () => {
+  const annotation = makeAnnotation();
+  const result = applyChangeToAnnotation(
+    annotation,
+    { rangeOffset: 10, rangeLength: 1, text: " " },
+    "abcdefghi"
+  );
+
+  assert.strictEqual(result, annotation);
+});
+
+test("case 5: shrinks or grows the end when the change is fully inside the annotation", () => {
+  const annotation = makeAnnotation();
+  const result = applyChangeToAnnotation(
+    annotation,
+    { rangeOffset: 6, rangeLength: 2, text: "wxyz" },
+    "abcdefghi"
+  );
+
+  assert.deepStrictEqual(result, {
+    ...annotation,
+    end: 12,
+  });
+});
+
+test("case 6: adjusts the start and end when the change overlaps the start of the annotation", () => {
+  const annotation = makeAnnotation();
+  const result = applyChangeToAnnotation(
+    annotation,
+    { rangeOffset: 2, rangeLength: 5, text: "XYZ" },
+    "abcdefghi"
+  );
+
+  assert.deepStrictEqual(result, {
+    ...annotation,
+    start: 2,
+    end: 8,
+  });
+});
+
+test("case 6 whitespace branch: anchors the new start to the inserted whitespace length", () => {
+  const annotation = makeAnnotation();
+  const result = applyChangeToAnnotation(
+    annotation,
+    { rangeOffset: 2, rangeLength: 5, text: "  " },
+    "abcdefghi"
+  );
+
+  assert.deepStrictEqual(result, {
+    ...annotation,
+    start: 4,
+    end: 7,
+  });
+});
+
+test("case 7: adjusts the end when the change overlaps the end of the annotation", () => {
+  const annotation = makeAnnotation();
+  const result = applyChangeToAnnotation(
+    annotation,
+    { rangeOffset: 8, rangeLength: 4, text: "XYZ" },
+    "abcdefghi"
+  );
+
+  assert.deepStrictEqual(result, {
+    ...annotation,
+    end: 11,
+  });
+});
+
+test("case 7 whitespace branch: snaps the end to the start of the overlapping change", () => {
+  const annotation = makeAnnotation();
+  const result = applyChangeToAnnotation(
+    annotation,
+    { rangeOffset: 8, rangeLength: 4, text: "  " },
+    "abcdefghi"
+  );
+
+  assert.deepStrictEqual(result, {
+    ...annotation,
+    end: 8,
+  });
+});
+
+test("case 8: collapses the annotation when the change fully contains it and removes the text", () => {
+  const annotation = makeAnnotation();
+  const result = applyChangeToAnnotation(
+    annotation,
+    { rangeOffset: 2, rangeLength: 10, text: "" },
+    "abcdefghi"
+  );
+
+  assert.deepStrictEqual(result, {
+    ...annotation,
+    start: 2,
+    end: 2,
+  });
+});
+
+test("case 8 whitespace branch: collapses the annotation when the change fully contains it and inserts whitespace", () => {
+  const annotation = makeAnnotation();
+  const result = applyChangeToAnnotation(
+    annotation,
+    { rangeOffset: 2, rangeLength: 10, text: "  " },
+    "abcdefghi"
+  );
+
+  assert.deepStrictEqual(result, {
+    ...annotation,
+    start: 2,
+    end: 2,
+  });
+});
\ No newline at end of file