fix: code review remediation - 97 findings resolved #33
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Complete specification for GitHub Issue #13: Multi-domain memory storage to distinguish between user-level (global) and project-level context. Specification includes: - REQUIREMENTS.md: 13 functional requirements (6 P0, 4 P1, 3 P2) - ARCHITECTURE.md: 9 component designs with data flow diagrams - IMPLEMENTATION_PLAN.md: 5 phases, 24 tasks - DECISIONS.md: 7 Architecture Decision Records - CHANGELOG.md: Specification evolution history Key decisions: - User memories in separate bare git repo (~/.local/share/memory-plugin/user-memories/) - Project memories override user memories on conflict - Team domain deferred to v2 - Optional remote auto-sync (opt-in via env vars) Closes #13 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Complete specification for LLM-powered subconsciousness layer: - REQUIREMENTS.md: 23 functional requirements (P0/P1/P2), success metrics - ARCHITECTURE.md: 7 components, schema extensions, LLM output templates - IMPLEMENTATION_PLAN.md: 6 phases, 85 tasks, verification gates - DECISIONS.md: 13 Architecture Decision Records Key features: - Provider-agnostic LLM client (Anthropic, OpenAI, Ollama) - Implicit capture with confidence thresholds - Semantic linking with 5 relationship types - Memory decay and intelligent forgetting - Consolidation into meta-memories - Proactive surfacing with rate limiting Grounded in CognitiveSubstrate research (Dual-Process Theory, SOAR/ACT-R). Closes #11 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Create PROGRESS.md with 24 tasks across 5 phases - Update README.md with approval and start timestamps - Update CHANGELOG.md with approval entry 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Task 1.1 complete - Add Domain Enum to Config Changes: - Add Domain enum with USER and PROJECT values - Add get_user_memories_path() for user-memories bare repo location - Add get_user_index_path() for user-domain SQLite index - Both functions support optional ensure_exists parameter for lazy dir creation - Add comprehensive tests for new configuration (17 tests) All 1851 tests pass, 88% coverage. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Add domain awareness to the Memory model for multi-domain storage: - Add `domain: str` field with default "project" for backward compatibility - Add `domain_enum` property to get Domain enum value - Add `is_user_domain` and `is_project_domain` convenience properties - Add domain properties to MemoryResult for uniform access - Add 7 tests covering domain field and properties Uses string storage for SQLite/JSON serialization compatibility, with enum property for type-safe programmatic access. Part of: SPEC-2025-12-25-001 (Multi-Domain Memories) Resolves: Task 1.2 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Phase 1 Foundation complete for multi-domain memories: Schema Migration (Task 1.3): - Bump SCHEMA_VERSION to 3 - Add domain TEXT column with 'project' default - Add idx_memories_domain index - Implement migration 3 for existing databases IndexService Domain (Task 1.4): - Update insert(), insert_batch(), update() for domain field - Update _row_to_memory() with backward-compatible domain reading Tests: - Add TestSchemaMigration class with v2→v3 migration test - Add fresh database schema test - Add domain-specific insert tests Closes phase 1 of SPEC-2025-12-25-001. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
…s 2.1-2.4) - Add GitOps.for_domain(domain) class method for domain-specific instances - Implement domain instance caching with clear_domain_cache() for testing - USER domain uses user-memories path, PROJECT domain uses repo path - Add ensure_user_repo_initialized() class method - Creates bare git repo at ~/.local/share/memory-plugin/user-memories/ - Configures git identity and creates initial empty commit - Add is_bare_repository() method for verification - Add optional domain parameter to search_vector() - Add optional domain parameter to search_text() - Both methods filter by domain when specified, backward compatible - Add domain filter to get_by_spec(), get_by_namespace(), list_recent() - Add domain filter to count() method - Update get_stats() to include by_domain breakdown - Add by_domain field and by_domain_dict property to IndexStats model Tests: 14 new GitOps tests, 13 new domain filter tests (1885 total, 89% coverage) 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Mark Tasks 2.1-2.4 as done in IMPLEMENTATION_PLAN.md - Update Phase 2 status to 100% done in PROGRESS.md - Add session notes for Phase 2 completion - Update current_phase to 2 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Apply 8 high-priority fixes from comprehensive code review: Security: - CRIT-001: Add ThreadPoolExecutor timeout (30s/120s) to embedding ops - SEC-HIGH-001: Add symlink verification before user-memories git init - SEC-HIGH-002: Add 64KB YAML size limit to prevent billion laughs - SEC-HIGH-003: Implement PID-based stale lock detection Performance: - PERF-HIGH-001: Add pagination (limit/offset) to get_all_ids() - PERF-HIGH-004: Add composite indexes for common query patterns Code Quality: - CRIT-003: Remove unused thread lock, document SQLite WAL concurrency - QUAL-HIGH-001: Replace 10 broad exception handlers with specific types Also removes code-review reports from docs/ (not needed in repo). 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Add noqa: ARG005 comments for unused lambda arguments in test mocks. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Add optional SecretsFilteringService integration to CaptureService - Filter both summary and content fields before storage - Rename MemoryError to MemoryPluginError (avoid shadowing builtin) - Add configurable secrets service injection - Replace suppress(Exception) with proper try-except logging - Add lock cleanup warning for debugging
* feat: initialize observability instrumentation implementation - Create PROGRESS.md with 29 tasks across 6 phases - Update README.md with started timestamp - Spec approved and ready for implementation Implements: SPEC-2025-12-25-001 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> * feat(observability): implement Phase 1 core infrastructure Complete observability foundation with: Core Modules: - config.py: ObservabilityConfig with env-based configuration - metrics.py: Thread-safe MetricsCollector (counters, histograms, gauges) - tracing.py: Span context with contextvars-based propagation - session.py: SessionIdentifier with privacy-preserving hashes - decorators.py: measure_duration decorator (sync/async support) - logging.py: StructuredLogger with JSON/text formatters Exporters: - prometheus.py: Prometheus text format (no external deps) - json_exporter.py: Full JSON export for metrics and traces Key Features: - Lazy imports via __getattr__ for hook performance (<5ms import) - Thread-safe operations with threading.Lock - Privacy-preserving SHA256 hashes (8 char truncated) - Histogram buckets aligned with hook timeouts (2s, 5s, 15s, 30s) - Rolling window for bounded memory in histograms Tests: - 115 new tests across 8 test modules - Coverage: 87.76% (above 80% threshold) - All quality gates passing Closes Phase 1 of SPEC-2025-12-25-001 (Observability Instrumentation) Ref: #10 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> * feat: Complete observability instrumentation (Phases 1-4) Implement comprehensive observability for git-notes-memory plugin: Phase 1 - Core Infrastructure: - MetricsCollector with counters, histograms, gauges (thread-safe) - SpanContext and trace_operation for distributed tracing - StructuredLogger with JSON/text formatters - SessionIdentifier for multi-tenant distinguishability - measure_duration decorator and timed_context Phase 2 - Service Instrumentation: - Instrument CaptureService, RecallService, EmbeddingService - Instrument IndexService, GitOps, Hook Handlers - Fix silent failure points with explicit logging and metrics - Add timed_hook_execution context manager Phase 3 - Structured Logging: - Add *args support to StructuredLogger for backwards compatibility - Migrate all 5 hook handlers to get_logger() - Migrate 7 hook support modules to structured logging Phase 4 - CLI & Export: - /memory:metrics command with text/json/prometheus formats - /memory:traces command with filtering options - /memory:health command with --timing for latency percentiles - PrometheusExporter class for Prometheus text format Phases 5-6 (OpenTelemetry, Docker stack) skipped as optional Tier 3. Closes #10 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> * fix: add exponential backoff and observability documentation MAXALL deep-clean remediation: - CRIT-001: Add exponential backoff with jitter to lock acquisition - Replaces fixed 100ms retry with 50ms→2s exponential backoff - Adds 0-10% jitter to prevent thundering herd - Reduces resource exhaustion risk under high concurrency - HIGH-004: Add composite index on (namespace, timestamp DESC) - Improves range query performance for get_by_namespace() - HIGH-014: Create docs/observability.md documentation - Metrics collection and Prometheus export - Tracing with span hierarchies - Structured logging configuration - Health checks and performance characteristics Code review artifacts in docs/code-review/2025/12/25/: - CODE_REVIEW.md: 90 findings from 9 specialist agents - REVIEW_SUMMARY.md: Executive summary - REMEDIATION_TASKS.md: Actionable checklist - REMEDIATION_REPORT.md: Final status with false positives All 1949 tests passing, 87.70% coverage. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> * feat(observability): add Docker Compose local observability stack Phase 6 implementation (tasks 6.1-6.2): - docker-compose.yml with OTEL Collector, Prometheus, Tempo, Loki, Grafana - OpenTelemetry Collector config with OTLP receivers and exporters - Prometheus scrape configuration for OTEL metrics - Tempo distributed tracing backend configuration - Loki log aggregation configuration - Grafana datasource provisioning (Prometheus, Tempo, Loki) - Grafana dashboard provisioning with auto-discovery - memory-operations.json dashboard (captures, searches, latency) - hook-performance.json dashboard (executions, timeouts, p95 latency) Exposed ports: - 3000: Grafana UI - 9090: Prometheus UI - 4317/4318: OTEL gRPC/HTTP - 3100: Loki - 3200: Tempo Usage: cd docker && docker-compose up -d 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> * fix(security): divest inline Python from command files into scripts Addresses PR #24 review comments: - SECURITY: Moved inline Python code from commands/*.md to scripts/*.py to prevent command injection via $ARGUMENTS string interpolation - scripts/metrics.py: Safe argument parsing via argparse/sys.argv - scripts/traces.py: Safe argument parsing via argparse/sys.argv - scripts/health.py: Safe argument parsing via argparse/sys.argv - Updated commands/metrics.md, traces.md, health.md to call scripts - Fixed exporters/__init__.py: explicit imports instead of lazy loading to resolve Copilot undefined export warnings The previous implementation embedded $ARGUMENTS directly into Python string literals, allowing code injection via crafted arguments. The new scripts pass arguments safely via command line. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> * feat(observability): implement OTLP HTTP exporter for telemetry push Completes Phase 5 of the observability spec by adding OTLP HTTP export capability so telemetry can be pushed to OpenTelemetry Collector and the Docker Compose observability stack. Changes: - New `exporters/otlp.py` with OTLPExporter class using stdlib only - Converts internal Span/metrics to OTLP JSON format - Pushes to {endpoint}/v1/traces and {endpoint}/v1/metrics - Configurable via MEMORY_PLUGIN_OTLP_ENDPOINT env var - Updated Stop handler to flush telemetry at session end - Updated observability.md with OTLP configuration section - Added comprehensive tests for OTLP exporter - pyproject.toml: added S310 per-file-ignore for OTLP file The exporter uses urllib.request (stdlib) to avoid adding dependencies. When MEMORY_PLUGIN_OTLP_ENDPOINT is set, traces and metrics are automatically exported when the Claude Code session ends. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>
- Fix connection leak on index initialization failure (CRIT-001) - Fix connection cleanup in session start hook (MED-001) - Add missing domain parameter to Memory creation in capture - Add composite index for status+timestamp queries (LOW-004)
- Add logger import to git_ops module - Log warning with exception details when batch fetch fails (LOW-010)
- Document all core, hook, secrets, and observability config options - Include example configurations for team, security, and debug modes - Reference remote sync and OpenTelemetry integration settings
- Add security-scan-on-edit hook for bandit security checks - Fix hook paths from git-notes-memory-manager to git-notes-memory - Update descriptions to reference CI workflow equivalents - Document all hooks in CLAUDE.md with CI mapping
- CODE_REVIEW.md: Full review report from 9 specialist agents - REMEDIATION_TASKS.md: Prioritized task list (all completed)
Add RULE 5 to all guidance templates (minimal, standard, detailed) that encourages Claude to search for relevant memories BEFORE modifying code, rather than relying solely on the ~5 generic memories injected at session start. Key additions: - RULE 5: PROACTIVE MEMORY SEARCH section with when/how to search - Failure mode warning for skipping proactive search - Self-audit reminder to search before major changes - Context explaining SessionStart relevance (~0.53) vs task-specific (~0.77+) This improves memory utilization by encouraging task-specific queries that yield much higher relevance scores than the generic project name search used at session initialization. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Use "./" prefix for source path (schema requirement) - Remove published plugin metadata (belongs in plugin.json) - Simplify to essential fields for local development install 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Implements Issue #11 subconsciousness layer with deep-clean remediation. - LLM client with circuit breaker pattern (3 states: CLOSED/OPEN/HALF_OPEN) - Multi-provider support (Anthropic, OpenAI, Ollama) - Implicit capture service for auto-detecting memory-worthy content - Adversarial prompt detection for security - Rate limiting with token bucket algorithm - Transcript chunking for large sessions Critical: - CRIT-001: Circuit breaker for LLM provider calls - CRIT-002: ServiceRegistry pattern replacing global mutable state High: - HIGH-001: Term limit (100) for O(n²) pattern matching - HIGH-002: sqlite-vec UPSERT limitation documented - HIGH-003: Composite index for common query pattern - HIGH-007: Jitter in exponential backoff - HIGH-008: PII scrubbing with 7 pattern types Medium: - MED-004: ANALYZE after VACUUM - MED-005: Context manager for SQLite connection - MED-007: Magic numbers to named constants - MED-008: Stale lock detection (5-minute threshold) - MED-011: Consent mechanism for PreCompact auto-capture - 2191 tests passing - 80.72% coverage - mypy --strict clean - ruff check clean 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Fix command injection vulnerability in commands/review.md by passing capture ID via environment variable instead of shell interpolation - Add explanatory comment to exception handler in implicit_capture_agent.py Security: - CVE-class shell injection fixed in --approve and --reject paths 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Project completed successfully with Phase 1-2 delivered: - LLM Foundation (provider-agnostic client) - Implicit Capture (auto-extraction with confidence scoring) Deliverables: - 134 tests (87%+ coverage) - 13 ADRs - Security fix (command injection) - PR #26 (open, ready for merge) Effort: ~14 hours (planned: 80-100 hours, -86% under budget) Scope: Phases 1-2 complete, Phases 3-6 deferred Artifacts moved to: docs/spec/completed/2025-12-25-llm-subconsciousness/ 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Critical fixes (4): - CRIT-001: secrets filtering bypass via YAML aliases - CRIT-002: command injection in git operations - CRIT-003: unbounded memory in embedding batch - CRIT-004: race condition in index initialization High priority fixes (23): - Security: input validation, error message sanitization - Performance: connection pooling, lazy loading, caching - Architecture: index module split into package - Test coverage: exception paths, edge cases Medium priority fixes (8 code changes): - Thread-safe user index initialization - Memory exhaustion prevention with file limits - Magic numbers extracted to constants - Type annotation accuracy improvements Remaining medium/low findings documented as BY DESIGN
New test files: - test_batcher.py: batch processing edge cases - test_llm_secrets_filtering.py: secrets in LLM responses - test_providers.py: LLM provider implementations - tests/hooks/: hook handler test suite Updated tests: - test_capture.py: lock retry constants - test_embedding.py: batch size limits, memory safety - test_index.py: refactored module imports - test_implicit_capture_agent.py: expanded coverage - test_otlp_exporter.py: OTLP configuration tests Coverage: 2860 tests, 85.51% coverage
Updated CODE_REVIEW.md: - Marked all findings with resolution status - Added verification checkmarks for completed items Updated REMEDIATION_TASKS.md: - All 97 findings tracked with completion status - Summary tables for each priority level - Code fix vs BY DESIGN classification
- marketplace.json: version bump - plugin.json: cleanup unused fields - hooks.json: adjust hook configurations - otel-collector-config.yaml: simplify OTLP settings
- Remove const_labels from Prometheus exporter configuration - Fixes "duplicate label names" error when resource attributes already contain service.name - Root cause: const_labels conflicted with resource processor attributes
- Add LogRecord dataclass for structured log entries - Add export_logs() method to OTLPExporter - Add export_logs_if_configured() convenience function - Integrate log export in stop_handler for session events - Logs include: session end summary, captured memories, uncaptured warnings - Data flow: Hook Events → LogRecord → OTLP → Loki → Grafana
- Add traces.json: Tempo traces dashboard with trace search, export rate - Add logs.json: Loki logs dashboard with log stream, volume by level, filtered views for errors and memory operations - Both dashboards auto-provisioned in "Git Notes Memory" folder
- Fix docker-compose.yml: document correct env vars (MEMORY_PLUGIN_OTLP_*) - Add SSRF override documentation (MEMORY_PLUGIN_OTLP_ALLOW_INTERNAL) - Add --export flag to metrics.py for manual OTLP export - Update metrics.md command help with export option - Update CLAUDE.md observability section
Add immediate metrics export after each operation instead of only at session end. This enables real-time monitoring in Grafana dashboards. Changes: - Add flush_metrics_to_otlp() helper in hook_utils.py - Export metrics after each capture in capture.py - Flush metrics before exit in all hook handlers - Add monitoring optional dependencies to pyproject.toml - Fix OTEL collector config for Loki integration 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Replace push_notes_to_remote() with sync_notes_with_remote(push=True) in the Stop hook to prevent race conditions in multi-worktree environments. The sync function implements fetch→merge→push workflow with cat_sort_uniq merge strategy, preventing non-fast-forward push failures when concurrent Claude sessions operate on the same repository. Fixes #28 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Replace filesystem-based script execution with direct Python module imports. This fixes marketplace plugin installations which use a different directory structure than source checkouts. - Observability: metrics.md, health.md, traces.md (inline module imports) - Core: capture.md, recall.md, search.md, status.md - Security: scan-secrets.md, secrets-allowlist.md, test-secret.md, audit-log.md - Sync: sync.md, validate.md, review.md Closes #31
Planning documents for Issue #31 including: - REQUIREMENTS.md with affected commands and success criteria - ARCHITECTURE.md with module import design pattern - IMPLEMENTATION_PLAN.md with 16 tasks across 5 phases - DECISIONS.md with 5 ADRs - PROGRESS.md tracking implementation status
The previous fix incorrectly removed --directory, which is needed for uv to find pyproject.toml when running from user project directory rather than the plugin directory. Corrected pattern uses CLAUDE_PLUGIN_ROOT directly without the broken fallback glob.
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Summary
Comprehensive code review remediation addressing all 97 findings from the deep-clean analysis, plus Issue #28 fix and observability enhancements.
Changes by Priority
Critical Fixes
High Priority Fixes
Medium Priority Fixes
Issue #28 Fix (cf64ea9)
push_notes_to_remote()withsync_notes_with_remote(push=True)in Stop hookdocs/spec/active/2025-12-26-multi-worktree-sync-fix/Observability Enhancements (446189b)
flush_metrics_to_otlp()helper in hook_utils.pyNew Tests
test_batcher.py: batch processing edge casestest_llm_secrets_filtering.py: secrets in LLM responsestest_providers.py: LLM provider implementationstests/hooks/: hook handler test suiteTest Plan
make qualitypasses (format, lint, typecheck, security)Related Issues