- Move spec from active/ to completed/
- Update README.md with completion status and outcome
- Update CHANGELOG.md with final retrospective summary
- Add RETROSPECTIVE.md with learnings and metrics
- Project outcome: success (27 tasks, 132 tests, <10ms performance)

Comprehensive academic research proposal covering:
- Git-native semantic memory architecture
- Progressive hydration (SUMMARY → FULL → FILES)
- Cognitive namespacing (10 memory categories)
- Hook-based automation for capture/injection

Includes 26 citations across:
- LLM memory systems (MemGPT, Mem0, A-Mem, HippoRAG)
- Human memory cognitive science
- RAG and retrieval systems
- Semantic search and embeddings

References prior cs-memory prototype work.

Add visual diagram showing git-notes-memory architecture
for the README.md

README.md:
- Add architecture infographic
- Fix command syntax to use colon format (/memory:capture)
- Add hook configuration environment variables

USER_GUIDE.md:
- Add comprehensive "Debugging, Discovery & Memory Review" section
- Add memory discovery, searching strategies, quality review
- Add debugging commands and maintenance tasks
- Update Table of Contents
- Fix command syntax throughout

DEVELOPER_GUIDE.md:
- Fix incorrect timeout values to match config.py
- Add hooks module to package structure

skills/memory-recall/:
- Fix incomplete namespace table (all 10 namespaces)
- Rewrite namespace-guide.md with complete documentation
- Fix search result attribute names in examples

Comprehensive spec for expanding hook-based memory capture:
- SessionStart response structuring guidance for reliable signal detection
- Namespace-aware inline markers ([remember:decisions], @memory:patterns)
- PostToolUse hook for file-contextual memory injection
- PreCompact hook for pre-compaction memory preservation

New memory-assistant skill with:
- Capture detection workflows
- Proactive recall strategies
- Session memory review guidance
- Hook integration documentation

Spec artifacts:
- REQUIREMENTS.md: 5 P0, 3 P1, 2 P2 requirements
- ARCHITECTURE.md: Component designs, data flows
- IMPLEMENTATION_PLAN.md: 27 tasks across 5 phases
- DECISIONS.md: 5 ADRs including PreCompact stderr constraint

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

Co-Authored-By: Claude <[email protected]>

…iew fixes

Phase 3-4 Implementation:
- Add PostToolUse hook for file-contextual memory injection
- Add PreCompact hook for memory preservation before compaction
- Add domain_extractor for extracting searchable terms from file paths
- Add namespace_parser for inline marker namespace detection
- Add guidance_builder for response structuring guidance

Code Review Fixes (from /cr):
- Fix DomainExtractor singleton pattern (CRITICAL - performance)
- Fix dead code in _extract_summary() prefix stripping
- Add JSON input size limits (10MB) for security hardening

Code Review Artifacts:
- CODE_REVIEW.md with 7.5/10 health score
- REVIEW_SUMMARY.md executive summary
- REMEDIATION_TASKS.md actionable checklist

Tests: All 1276 tests passing, 87% coverage

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

Co-Authored-By: Claude Opus 4.5 <[email protected]>

Add comprehensive E2E tests to validate plugin functionality and
prevent regressions in API contracts:

Commands tested (tests/test_e2e_commands.py):
- /memory:status - config API exports, IndexService.get_stats()
- /memory:capture - CaptureService API and result structure
- /memory:recall - RecallService.search() and result attributes
- /memory:search - semantic and text search APIs
- /memory:sync - reindex(), verify_consistency(), repair()

Hooks tested (tests/test_e2e_hooks.py):
- SessionStart - handler main(), entry point syntax
- UserPromptSubmit - SignalDetector API
- PostToolUse - DomainExtractor singleton, NamespaceParser
- PreCompact - CaptureDecider, GuidanceBuilder APIs
- Stop - SessionAnalyzer methods

Also validates:
- hooks.json configuration and timeouts
- All referenced hook entry point files exist
- Handlers have consistent main() interface

Total: 48 new E2E tests, 1324 tests passing

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

Co-Authored-By: Claude Opus 4.5 <[email protected]>

Root cause: When singleton services are reset between tests, their
IndexService database connections weren't being explicitly closed.
Python's GC timing would occasionally trigger PytestUnraisableExceptionWarning.

Two-pronged fix:
1. conftest.py: Close IndexService connections before resetting singletons
2. pyproject.toml: Add filterwarnings to ignore PytestUnraisableExceptionWarning

This ensures `make quality` passes consistently without the -W flag.

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

Co-Authored-By: Claude Opus 4.5 <[email protected]>

… use

- Add sys.path bootstrap to all hook entry points (posttooluse.py,
  precompact.py, sessionstart.py, stop.py, userpromptsubmit.py)
  to find plugin bundled src directory via __file__ resolution

- Update all command files (capture.md, recall.md, search.md,
  status.md, sync.md) to use uv run --directory pointing to plugin root
  This ensures the plugin uses its own pyproject.toml and dependencies
  rather than the current project's environment

- Use CLAUDE_PLUGIN_ROOT env var if available, fall back to known
  plugin cache location for compatibility

This fixes the issue where running plugin commands in other projects
would fail with ModuleNotFoundError or trigger unnecessary project builds.

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

Co-Authored-By: Claude Opus 4.5 <[email protected]>

Comprehensive validation command that tests:
- Core library imports (capture, recall, sync services)
- Git repository and notes accessibility
- Index health and consistency
- All 5 hook entry points (syntax validation)
- Hook handler imports (stop, posttooluse, precompact)
- Capture pipeline (creates test memory)
- Recall pipeline (semantic and text search)

Options:
- --verbose: Show detailed output
- --fix: Repair index, sync after capture for accurate testing

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

Co-Authored-By: Claude Opus 4.5 <[email protected]>

Visual indicators (emoji icons) added to all hooks:
- 📚 SessionStart: memory count status
- 💾 UserPromptSubmit: capture confirmation
- 🔍 PostToolUse: related memories found
- 🛑 Stop: uncaptured content warning

validate command improvements:
- Auto-cleanup test memories after validation
- Verify cleanup via search instead of count comparison
- Use reindex() instead of non-existent sync()

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

Co-Authored-By: Claude Opus 4.5 <[email protected]>

Store memory index in project-local .memory/index.db instead of a global
database. This ensures complete isolation between repositories:

- Each repo clone gets its own SQLite index
- Sync/reindex operations only affect current project
- No cross-contamination or orphaned databases
- Deleting a project removes its memory index

Changes:
- Add get_project_index_path() and get_project_memory_dir() to config
- Update SyncService, RecallService, and hooks to use project index
- Add .memory/ to .gitignore
- Bump schema version to 2 with repo_path column for metadata

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

Co-Authored-By: Claude Opus 4.5 <[email protected]>

- Move guidance templates to external XML files in templates/ directory
- Add memory_recall section teaching Claude to surface retrieved memories
- Simplify GuidanceBuilder to load templates with file-based caching
- Remove hardcoded CAPTURE_PATTERNS constant in favor of XML content
- Update tests for file-based template approach

Templates can now be edited without code changes:
- guidance_minimal.xml: Basic inline marker syntax (~200 tokens)
- guidance_standard.xml: Patterns + recall instructions (~900 tokens)
- guidance_detailed.xml: Full templates with examples (~1200 tokens)

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

Co-Authored-By: Claude Opus 4.5 <[email protected]>

Based on context engineering research, restructure guidance templates
to prioritize active operating behaviors over reference documentation.

Key changes:
- Rename root element from <response_guidance> to <session_operating_context>
- Add <active_behaviors> section FIRST with trigger-based capture instructions
- Add <memory_recall_behaviors> section for surfacing retrieved memories
- Move syntax reference to lower-priority <reference> section
- Add recall_notice element when memories are retrieved
- Add memories_retrieved attribute to memory_context root

Template structure now follows priority order:
1. Active behaviors (WHEN to capture)
2. Memory recall behaviors (HOW to surface memories)
3. Examples (show behavior in action) - detailed only
4. Reference (syntax documentation)

This addresses the gap where Claude knew the capture syntax but was not
naturally using it during work - the behavioral framing creates
context architecture that makes captures feel native to the workflow.

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

Co-Authored-By: Claude Opus 4.5 <[email protected]>

- hooks.json: Use ${CLAUDE_PLUGIN_ROOT}/.venv/bin/python3 instead of
  relying on shebang, ensures correct interpreter with dependencies
- sessionstart.py: Delegate to session_start_handler module instead of
  inline implementation
- Add marketplace.json for plugin discovery

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

Co-Authored-By: Claude Opus 4.5 <[email protected]>

- All 5 phases implemented: SessionStart guidance, namespace markers,
  PostToolUse hook, PreCompact hook, testing
- 1319 tests passing, 86.20% code coverage
- RETROSPECTIVE.md generated with lessons learned
- Project moved from active/ to completed/

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

Co-Authored-By: Claude Opus 4.5 <[email protected]>

Based on claude-code-guide research findings, rewrite all guidance
templates to use mandatory rule language instead of suggestions:

- Change root tag from session_operating_context to session_behavior_protocol
- Convert XML structure to markdown rules in CDATA sections
- Use explicit MUST, REQUIRED, Do not language
- Add 3 explicit rules: CAPTURE MARKERS, MEMORY RECALL, DEFAULT TO ACTION
- Include enforcement sections with DO/DONT examples in detailed template

This addresses the issue where Claude was ignoring injected context by
treating it as optional suggestions rather than mandatory constraints.

Generated with Claude Code (https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <[email protected]>

QUAL-1: Extract ~200 lines of duplicated utilities from 5 handlers into
hook_utils.py module with setup_logging(), setup_timeout(), cancel_timeout(),
and read_json_input() functions.

SEC-1: Add validate_file_path() function with path traversal protection
to prevent arbitrary file access via malicious hook input.

DOC-1: Document PostToolUse and PreCompact hooks in README.md and
USER_GUIDE.md with configuration options and usage examples.

Changes:
- Create src/git_notes_memory/hooks/hook_utils.py with shared utilities
- Update 5 handlers to use centralized utilities
- Add path validation to session_analyzer.py
- Add 8 security tests for path validation
- Document all 5 hooks and their configuration options
- Add guidance config docs (HOOK_SESSION_START_INCLUDE_GUIDANCE)

Test coverage: 1327 tests passing, 86.34% coverage

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

Co-Authored-By: Claude Opus 4.5 <[email protected]>