Implement Copy-on-Write (CoW) cloning support and migration middleware

Major features added:
- Migration middleware system with real-time detection and state tracking
- @requires_qdrant_access decorator applied to 8 CLI commands
- force-flush command for CoW operations with multi-filesystem examples
- Comprehensive E2E test for complete CoW clone workflow
- Async-safe operations and deadlock prevention
- Enhanced CLI help with BTRFS, ZFS, and XFS examples
- Full automation integration with configurable CoW test inclusion

Technical improvements:
- Snapshot API integration for reliable data flushing
- Project isolation through local storage directories
- Robust error handling for test environments
- Aggressive setup pattern for better test performance

Version bump: 1.0.0.7 → 1.1.0.0

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <noreply@anthropic.com>

Author: jsbattig

.github/workflows/main.yml

@@ -83,6 +83,11 @@ jobs:
           --ignore=tests/test_chunker_docstring_fix.py \
           --ignore=tests/test_prompt_formatting_issues.py \
           --ignore=tests/test_parallel_voyage_performance.py \
+          --ignore=tests/test_branch_transition_logic_fix.py \
+          --ignore=tests/test_compare_search_methods.py \
+          --ignore=tests/test_debug_branch_isolation.py \
+          --ignore=tests/test_search_with_branch_topology_fix.py \
+          --ignore=tests/test_cow_clone_e2e_full_automation.py \
           -m "not slow and not e2e and not real_api" \
           --cov=src/code_indexer --cov-report=xml --cov-report=term
     

CLAUDE.md

@@ -51,4 +51,5 @@
 - When working on improvements for the smart indexer, always consider the --reconcile function (non git-aware) and ensure consistency across both indexing processes. Treat the --reconcile aspect as equally important, maintaining feature parity and functionality, except for semantically specific module considerations.
 - NEVER, EVER, remove functionality related to our enhanced processing of git projects. The git-awarness aspects, how we optimize processing branches, and keeping track of relationships, deduplication of indexing is what make this project unique. If you ever go into a refactoring rabbit hole and you will start removing functionality to that enables this capability you must stop, immediately, and ask if that's the true intent of the work you been asked to do.
 - When working on fixing quick feedback unit tests, or fast tests, always use ./ci-github.sh. This shell file is specifically tuned to run test that run fast, so they can be run efficiently from within Claude Code as a first layer of protection ensuring our tests pass and we didn't introduce regressions.
-- When indexing, progress reporting is done real-time, in a single line at the bottom, showing a progress bar, and right next to it we show speed metrics and current file being processed. Don't change this approach without confirmation from the user. This is how it is, and it should be for all indexing operations, we don't show feedback scrolling the console, EVER, NEVER, EVER. Ask for confirmation if you are about to change this behavior. If the user ask you to change it, ask question, confirm the user is sure it wants to remove the single line, fixed to the bottom, progress bar, speed and currently file being processed.
+- When indexing, progress reporting is done real-time, in a single line at the bottom, showing a progress bar, and right next to it we show speed metrics and current file being processed. Don't change this approach without confirmation from the user. This is how it is, and it should be for all indexing operations, we don't show feedback scrolling the console, EVER, NEVER, EVER. Ask for confirmation if you are about to change this behavior. If the user ask you to change it, ask question, confirm the user is sure it wants to remove the single line, fixed to the bottom, progress bar, speed and currently file being processed.
+- When asking to bump version, you will always check readme in case there's references to the version number, and you will always updte the release notes files with the latest changes

RELEASE_NOTES.md

@@ -1,5 +1,42 @@
 # Code Indexer Release Notes
 
+## Version 1.1.0.0 (2025-01-05)
+
+### 🚀 Major Feature: Copy-on-Write (CoW) Clone Support
+
+#### **Migration Middleware System**
+- **Real-time Migration Detection**: Automatically detects when indexed projects are CoW clones and handles migration gracefully
+- **Migration State Tracking**: Persistent state tracking across system restarts with async-safe operations
+- **Decorator Integration**: `@requires_qdrant_access` decorator automatically applied to all Qdrant-dependent CLI commands
+- **Deadlock Prevention**: Fixed critical async deadlock in migration state management
+
+#### **CoW Operations Support**
+- **Force-flush Command**: New `force-flush` command ensures data consistency before CoW cloning
+- **Multi-filesystem Support**: Comprehensive examples for BTRFS, ZFS, and XFS filesystems
+- **Project Isolation**: Proper handling of local storage directories for cloned projects
+- **Configuration Migration**: Automatic config fixing for cloned projects
+
+#### **Enhanced CLI Integration**
+- **8 Commands Protected**: Applied migration middleware to index, query, claude, watch, status, optimize, schema, and start commands
+- **Comprehensive Help**: Added detailed CoW cloning examples and workflow documentation
+- **Error Handling**: Robust error handling for missing directories and test environments
+
+#### **Testing Infrastructure**
+- **E2E CoW Test**: Comprehensive 10-phase end-to-end test for complete CoW clone workflow
+- **Aggressive Setup Pattern**: Tests use shared services for better performance while maintaining isolation
+- **Full Automation Integration**: CoW tests included in full-automation.sh by default
+
+### 📊 Technical Implementation
+- **Async-safe Operations**: All migration operations designed for concurrent access
+- **Snapshot API Integration**: Uses Qdrant snapshot API for reliable data flushing
+- **Project Path Flexibility**: Supports both current directory and explicit project path specifications
+- **Cleanup Management**: Automatic cleanup of temporary snapshots and migration artifacts
+
+### 🔧 Developer Experience
+- **Example Workflows**: Complete documentation of CoW cloning processes for different filesystems
+- **Integration Testing**: Comprehensive test coverage for migration scenarios
+- **Performance Optimized**: Minimal overhead for non-CoW operations
+
 ## Version 1.0.0.7 (2025-01-04)
 
 ### 🧪 Testing Infrastructure Improvements

ci-github.sh

@@ -130,6 +130,7 @@ if pytest tests/ \
     --ignore=tests/test_compare_search_methods.py \
     --ignore=tests/test_debug_branch_isolation.py \
     --ignore=tests/test_search_with_branch_topology_fix.py \
+    --ignore=tests/test_cow_clone_e2e_full_automation.py \
     -m "not slow and not e2e and not real_api" \
     --cov=src/code_indexer --cov-report=xml --cov-report=term; then
     print_success "Unit tests passed"
@@ -167,6 +168,7 @@ echo "   • Docker Compose validation tests (require Docker)"
 echo "   • Idempotent setup tests (require Docker services)"
 echo "   • Branch topology E2E tests (require Git and indexing services)"
 echo "   • Schema migration E2E tests (require Qdrant and embedding services)"
+echo "   • CoW clone E2E tests (require CoW filesystem and real services)"
 echo "   • Optimized example tests (require Docker and VoyageAI API)"
 echo "   • Comprehensive git workflow tests (require full service stack)"
 echo "   • Git-aware watch E2E tests (require service dependencies)"

full-automation.sh

@@ -89,11 +89,26 @@ fi
 
 # 6. Run tests with coverage
 print_step "Running tests with coverage"
-if pytest tests/ --cov=src/code_indexer --cov-report=xml --cov-report=term; then
-    print_success "All tests passed"
+
+# Check if COW_CLONE_E2E_TESTS is set to exclude the slow CoW clone tests
+if [[ "${COW_CLONE_E2E_TESTS:-}" == "false" ]]; then
+    print_warning "Skipping CoW clone E2E tests (COW_CLONE_E2E_TESTS=false)"
+    # Exclude the specific CoW clone test to speed up the run
+    if pytest tests/ --ignore=tests/test_cow_clone_e2e_full_automation.py --cov=src/code_indexer --cov-report=xml --cov-report=term; then
+        print_success "All tests passed (excluding CoW clone E2E test)"
+    else
+        print_error "Tests failed"
+        exit 1
+    fi
 else
-    print_error "Tests failed"
-    exit 1
+    print_step "Including CoW clone E2E tests (may take several minutes)"
+    print_step "To skip them: export COW_CLONE_E2E_TESTS=false"
+    if pytest tests/ --cov=src/code_indexer --cov-report=xml --cov-report=term; then
+        print_success "All tests passed (including CoW clone E2E)"
+    else
+        print_error "Tests failed (including CoW clone E2E)"
+        exit 1
+    fi
 fi
 
 # 7. Build package