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+## Description
+
+Fixes #5655
+
+This PR resolves three critical issues with codebase indexing file exclusion rules that were preventing .gitignore and .rooignore files from working correctly.
+
+## Issues Fixed
+
+### 1. .gitignore files have no effect on indexing
+
+**Root Cause**: The manager was trying to read a single `.gitignore` file without checking existence, causing silent failures.
+
+**Solution**: Replaced broken logic with proper use of `findGitignoreFiles()` function that walks up the directory tree to find all .gitignore files and loads patterns correctly.
+
+### 2. .rooignore files only work after VSCode restart and are inconsistent
+
+**Root Cause**: Each scan was creating new `RooIgnoreController` instances without file watchers, losing ignore patterns.
+
+**Solution**: Created a global `RooIgnoreController` instance in the manager that is reused across all components, ensuring file watchers and patterns are preserved.
+
+### 3. .rooignore rules are ignored after using 'Clear Index Data' until VSCode restart
+
+**Root Cause**: Service recreation during "Clear Index Data" wasn't reloading ignore patterns.
+
+**Solution**: Made `loadRooIgnore()` method public and ensured patterns are reloaded during service recreation.
+
+## Changes Made
+
+- **src/services/code-index/manager.ts**:
+
+    - Added global `_rooIgnoreController` instance
+    - Fixed .gitignore loading to use `findGitignoreFiles()` instead of broken single-file logic
+    - Added proper initialization and disposal of RooIgnoreController
+    - Ensured patterns are reloaded during service recreation
+
+- **src/core/ignore/RooIgnoreController.ts**:
+
+    - Made `loadRooIgnore()` method public for external reloading
+    - Fixed `dispose()` method to handle undefined disposables safely
+
+- **src/services/code-index/processors/scanner.ts**:
+
+    - Updated constructor to accept optional `RooIgnoreController` parameter
+    - Modified logic to use injected controller instead of creating new instances
+
+- **src/services/code-index/service-factory.ts**:
+
+    - Updated factory methods to accept and pass `RooIgnoreController`
+    - Ensured global controller is used by both scanner and file watcher
+
+- **src/services/glob/list-files.ts**:
+    - Exported `findGitignoreFiles()` function for use in manager
+
+## Testing
+
+- **Added comprehensive integration tests** in `src/services/code-index/__tests__/ignore-integration.spec.ts` covering:
+
+    - .gitignore pattern loading and application
+    - RooIgnoreController instance preservation across service recreations
+    - Pattern reloading during service recreation
+    - Integration between gitignore and rooignore controllers
+
+- **Fixed existing test infrastructure**:
+
+    - Updated VSCode mocks to include `RelativePattern` and `createFileSystemWatcher`
+    - Fixed test mocks to properly simulate initialized manager state
+
+- **All tests passing**:
+    - ✅ 5/5 new integration tests pass
+    - ✅ 346/346 code-index tests pass (no regressions)
+    - ✅ All linting and type checking passes
+
+## Verification of Acceptance Criteria
+
+- [x] **.gitignore files now have effect on indexing**: Fixed broken loading logic
+- [x] **.rooignore files work consistently without VSCode restart**: Global controller instance preserves patterns and file watchers
+- [x] **.rooignore rules persist after "Clear Index Data"**: Patterns are properly reloaded during service recreation
+- [x] **All existing functionality preserved**: No breaking changes, backward compatible
+- [x] **Comprehensive test coverage**: Integration tests verify all three issues are resolved
+
+## Checklist
+
+- [x] Code follows project style guidelines
+- [x] Self-review completed
+- [x] Comments added for complex logic
+- [x] No breaking changes
+- [x] All tests pass (346/346 code-index tests)
+- [x] Linting and type checking pass
+- [x] Integration tests added for all reported issues
+- [x] Backward compatibility maintained