Fix/grep dedup

.gitignore

@@ -1,2 +1,3 @@
 /target
 
+.serena/*

.serena/project.yml

@@ -3,18 +3,16 @@ project_name: "code-mcp"
 
 
 # list of languages for which language servers are started; choose from:
-#   al                  ansible             bash                clojure             cpp
-#   cpp_ccls            crystal             csharp              csharp_omnisharp    dart
-#   elixir              elm                 erlang              fortran             fsharp
-#   go                  groovy              haskell             haxe                hlsl
-#   java                json                julia               kotlin              lean4
-#   lua                 luau                markdown            matlab              msl
-#   nix                 ocaml               pascal              perl                php
-#   php_phpactor        powershell          python              python_jedi         python_ty
-#   r                   rego                ruby                ruby_solargraph     rust
-#   scala               solidity            swift               systemverilog       terraform
-#   toml                typescript          typescript_vts      vue                 yaml
-#   zig
+#   al                  bash                clojure             cpp                 csharp
+#   csharp_omnisharp    dart                elixir              elm                 erlang
+#   fortran             fsharp              go                  groovy              haskell
+#   haxe                java                julia               kotlin              lua
+#   markdown
+#   matlab              nix                 pascal              perl                php
+#   php_phpactor        powershell          python              python_jedi         r
+#   rego                ruby                ruby_solargraph     rust                scala
+#   swift               terraform           toml                typescript          typescript_vts
+#   vue                 yaml                zig
 #   (This list may be outdated. For the current list, see values of Language enum here:
 #   https://github.com/oraios/serena/blob/main/src/solidlsp/ls_config.py
 #   For some languages, there are alternative language servers, e.g. csharp_omnisharp, ruby_solargraph.)
@@ -68,27 +66,61 @@ read_only: false
 
 # list of tool names to exclude.
 # This extends the existing exclusions (e.g. from the global configuration)
-# Find the list of tools here: https://oraios.github.io/serena/01-about/035_tools.html
+#
+# Below is the complete list of tools for convenience.
+# To make sure you have the latest list of tools, and to view their descriptions, 
+# execute `uv run scripts/print_tool_overview.py`.
+#
+#  * `activate_project`: Activates a project based on the project name or path.
+#  * `check_onboarding_performed`: Checks whether project onboarding was already performed.
+#  * `create_text_file`: Creates/overwrites a file in the project directory.
+#  * `delete_memory`: Delete a memory file. Should only happen if a user asks for it explicitly,
+#       for example by saying that the information retrieved from a memory file is no longer correct
+#       or no longer relevant for the project.
+#  * `edit_memory`: Replaces content matching a regular expression in a memory.
+#  * `execute_shell_command`: Executes a shell command.
+#  * `find_file`: Finds files in the given relative paths
+#  * `find_referencing_symbols`: Finds symbols that reference the given symbol using the language server backend
+#  * `find_symbol`: Performs a global (or local) search using the language server backend.
+#  * `get_current_config`: Prints the current configuration of the agent, including the active and available projects, tools, contexts, and modes.
+#  * `get_symbols_overview`: Gets an overview of the top-level symbols defined in a given file.
+#  * `initial_instructions`: Provides instructions Serena usage (i.e. the 'Serena Instructions Manual')
+#       for clients that do not read the initial instructions when the MCP server is connected.
+#  * `insert_after_symbol`: Inserts content after the end of the definition of a given symbol.
+#  * `insert_before_symbol`: Inserts content before the beginning of the definition of a given symbol.
+#  * `list_dir`: Lists files and directories in the given directory (optionally with recursion).
+#  * `list_memories`: List available memories. Any memory can be read using the `read_memory` tool.
+#  * `onboarding`: Performs onboarding (identifying the project structure and essential tasks, e.g. for testing or building).
+#  * `read_file`: Reads a file within the project directory.
+#  * `read_memory`: Read the content of a memory file. This tool should only be used if the information
+#       is relevant to the current task. You can infer whether the information
+#       is relevant from the memory file name.
+#       You should not read the same memory file multiple times in the same conversation.
+#  * `rename_memory`: Renames or moves a memory. Moving between project and global scope is supported
+#       (e.g., renaming "global/foo" to "bar" moves it from global to project scope).
+#  * `rename_symbol`: Renames a symbol throughout the codebase using language server refactoring capabilities.
+#       For JB, we use a separate tool.
+#  * `replace_content`: Replaces content in a file (optionally using regular expressions).
+#  * `replace_symbol_body`: Replaces the full definition of a symbol using the language server backend.
+#  * `safe_delete_symbol`:
+#  * `search_for_pattern`: Performs a search for a pattern in the project.
+#  * `write_memory`: Write some information (utf-8-encoded) about this project that can be useful for future tasks to a memory in md format.
+#       The memory name should be meaningful.
 excluded_tools: []
 
 # list of tools to include that would otherwise be disabled (particularly optional tools that are disabled by default).
 # This extends the existing inclusions (e.g. from the global configuration).
-# Find the list of tools here: https://oraios.github.io/serena/01-about/035_tools.html
 included_optional_tools: []
 
 # fixed set of tools to use as the base tool set (if non-empty), replacing Serena's default set of tools.
 # This cannot be combined with non-empty excluded_tools or included_optional_tools.
-# Find the list of tools here: https://oraios.github.io/serena/01-about/035_tools.html
 fixed_tools: []
 
-# list of mode names that are to be activated by default, overriding the setting in the global configuration.
-# The full set of modes to be activated is base_modes (from global config) + default_modes + added_modes.
-# If the setting is undefined/empty, the default_modes from the global configuration (serena_config.yml) apply.
+# list of mode names that are to be activated by default.
+# The full set of modes to be activated is base_modes + default_modes.
+# If the setting is undefined, the default_modes from the global configuration (serena_config.yml) apply.
 # Otherwise, this overrides the setting from the global configuration (serena_config.yml).
-# Therefore, you can set this to [] if you do not want the default modes defined in the global config to apply
-# for this project.
 # This setting can, in turn, be overridden by CLI parameters (--mode).
-# See https://oraios.github.io/serena/02-usage/050_configuration.html#modes
 default_modes:
 
 # list of mode names to be activated additionally for this project, e.g. ["query-projects"]
@@ -128,3 +160,11 @@ ignored_memory_patterns: []
 #     - ../sibling-package
 #     - ../shared-lib
 additional_workspace_folders: []
+
+# list of mode names to that are always to be included in the set of active modes
+# The full set of modes to be activated is base_modes + default_modes.
+# If the setting is undefined, the base_modes from the global configuration (serena_config.yml) apply.
+# Otherwise, this setting overrides the global configuration.
+# Set this to [] to disable base modes for this project.
+# Set this to a list of mode names to always include the respective modes for this project.
+base_modes:

src/tools/common.rs

@@ -4,7 +4,6 @@
 use super::options::GrepOptions;
 use ignore::WalkBuilder;
 use std::path::Path;
-use std::sync::atomic::{AtomicUsize, Ordering};
 use std::sync::mpsc::Receiver;
 use std::sync::Mutex;
 
@@ -42,22 +41,7 @@ pub(crate) fn extension_matches(path: &Path, extensions: &[String]) -> bool {
         .is_some_and(|e| extensions.iter().any(|w| w == e))
 }
 
-/// Collect shared error state into the final `ToolResponse` metadata fields.
-pub(crate) fn error_metadata(
-    entry_errors: &AtomicUsize,
-    search_errors: &AtomicUsize,
-    first_entry_err: &Mutex<Option<String>>,
-    first_search_err: &Mutex<Option<String>>,
-) -> (usize, usize, Option<String>) {
-    let entry_err_n = entry_errors.load(Ordering::Relaxed);
-    let search_err_n = search_errors.load(Ordering::Relaxed);
-    let first_error = first_entry_err
-        .lock()
-        .ok()
-        .and_then(|g| g.clone())
-        .or_else(|| first_search_err.lock().ok().and_then(|g| g.clone()));
-    (entry_err_n, search_err_n, first_error)
-}
+
 
 /// Drain string chunks from `rx` into a single output buffer, enforcing the
 /// authoritative `max_bytes` cap. When the cap is hit the final chunk is cut on