fix(config): address CodeRabbit review comments

- Guard dict/scalar type conflict in _type_based_merge: when base holds
  a scalar or list for a key that an overlay wants to replace with a
  dict, let the overlay win outright instead of recursing into a non-dict
  (which crashes with TypeError before validation can surface a ConfigError)

- Add integration test verifying _load_scoped auto-gitignores
  config.local.toml when the file is present (test_load_scoped_gitignores_local_config)

- Add MD041-compliant H1 heading to agents/default/system.md

Author: elkaix

src/pythinker_code/agents/default/system.md

@@ -1,3 +1,5 @@
+# System Prompt
+
 You are **Pythinker** — a think-first software engineering agent developed by **Pythoughts-labs**, running on the user's computer. Before you write code, you read code.
 
 ## Product Identity

src/pythinker_code/config.py

@@ -159,6 +159,12 @@ def _type_based_merge(
     """
     for key, value in overlay.items():
         if isinstance(value, dict):
+            # If base holds a scalar/list for this key, the overlay dict wins outright
+            # (recursing into a non-dict crashes with TypeError before validation runs).
+            if key in base and not isinstance(base[key], dict):
+                base[key] = value
+                provenance[key] = scope
+                continue
             # For dicts, always recurse to track individual nested keys
             if key not in base:
                 base[key] = {}

tests/core/test_config.py

@@ -597,6 +597,19 @@ def test_load_scoped_source_scopes_populated(tmp_path, monkeypatch):
     assert "local" not in config.source_scopes  # local file absent
 
 
+def test_load_scoped_gitignores_local_config(tmp_path, monkeypatch):
+    monkeypatch.setenv("PYTHINKER_SHARE_DIR", str(tmp_path))
+    _write_toml(tmp_path / "config.toml", {})
+    project_root = tmp_path / "myproject"
+    _write_toml(project_root / ".pythinker" / "config.local.toml", {})
+
+    _load_scoped(project_root=project_root)
+
+    gitignore = project_root / ".gitignore"
+    assert gitignore.exists()
+    assert ".pythinker/config.local.toml" in gitignore.read_text(encoding="utf-8")
+
+
 def test_load_config_explicit_path_bypasses_scoping(tmp_path):
     """--config flag must bypass scope resolution entirely."""
     config_file = tmp_path / "explicit.toml"