* docs: add investigation reports for 5 open GitHub issues
Comprehensive analysis of issues #543, #544, #545, #555, and #557:
- #557: settings.json not generated, module loader error (node/bun mismatch)
- #555: Windows hooks not executing, hasIpc always false
- #545: formatTool crashes on non-JSON tool_input strings
- #544: mem-search skill hint shown incorrectly to Claude Code users
- #543: /claude-mem slash command unavailable despite installation
Each report includes root cause analysis, affected files, and proposed fixes.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
* fix(logger): handle non-JSON tool_input in formatTool (#545)
Wrap JSON.parse in try-catch to handle raw string inputs (e.g., Bash
commands) that aren't valid JSON. Falls back to using the string as-is.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
* fix(context): update mem-search hint to reference MCP tools (#544)
Update hint messages to reference MCP tools (search, get_observations)
instead of the deprecated "mem-search skill" terminology.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
* fix(settings): auto-create settings.json on first load (#557, #543)
When settings.json doesn't exist, create it with defaults instead of
returning in-memory defaults. Creates parent directory if needed.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
* fix(hooks): use bun runtime for hooks except smart-install (#557)
Change hook commands from node to bun since hooks use bun:sqlite.
Keep smart-install.js on node since it bootstraps bun installation.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
* chore: rebuild plugin scripts
* docs: clarify that build artifacts must be committed
* fix(docs): update build artifacts directory reference in CLAUDE.md
* test: add test coverage for PR #558 fixes
- Fix 2 failing tests: update "mem-search skill" → "MCP tools" expectations
- Add 56 tests for formatTool() JSON.parse crash fix (Issue #545)
- Add 27 tests for settings.json auto-creation (Issue #543)
Test coverage includes:
- formatTool: JSON parsing, raw strings, objects, null/undefined, all tool types
- Settings: file creation, directory creation, schema migration, edge cases
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
* fix(tests): clean up flaky tests and fix circular dependency
Phase 1 of test quality improvements:
- Delete 6 harmful/worthless test files that used problematic mock.module()
patterns or tested implementation details rather than behavior:
- context-builder.test.ts (tested internal implementation)
- export-types.test.ts (fragile mock patterns)
- smart-install.test.ts (shell script testing antipattern)
- session_id_refactor.test.ts (outdated, tested refactoring itself)
- validate_sql_update.test.ts (one-time migration validation)
- observation-broadcaster.test.ts (excessive mocking)
- Fix circular dependency between logger.ts and SettingsDefaultsManager.ts
by using late binding pattern - logger now lazily loads settings
- Refactor mock.module() to spyOn() in several test files for more
maintainable and less brittle tests:
- observation-compiler.test.ts
- gemini_agent.test.ts
- error-handler.test.ts
- server.test.ts
- response-processor.test.ts
All 649 tests pass.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
* refactor(tests): phase 2 - reduce mock-heavy tests and improve focus
- Remove mock-heavy query tests from observation-compiler.test.ts, keep real buildTimeline tests
- Convert session_id_usage_validation.test.ts from 477 to 178 lines of focused smoke tests
- Remove tests for language built-ins from worker-spawn.test.ts (JSON.parse, array indexing)
- Rename logger-coverage.test.ts to logger-usage-standards.test.ts for clarity
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
* docs(tests): phase 3 - add JSDoc mock justification to test files
Document mock usage rationale in 5 test files to improve maintainability:
- error-handler.test.ts: Express req/res mocks, logger spies (~11%)
- fallback-error-handler.test.ts: Zero mocks, pure function tests
- session-cleanup-helper.test.ts: Session fixtures, worker mocks (~19%)
- hook-constants.test.ts: process.platform mock for Windows tests (~12%)
- session_store.test.ts: Zero mocks, real SQLite :memory: database
Part of ongoing effort to document mock justifications per TESTING.md guidelines.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
* test(integration): phase 5 - add 72 tests for critical coverage gaps
Add comprehensive test coverage for previously untested areas:
- tests/integration/hook-execution-e2e.test.ts (10 tests)
Tests lifecycle hooks execution flow and context propagation
- tests/integration/worker-api-endpoints.test.ts (19 tests)
Tests all worker service HTTP endpoints without heavy mocking
- tests/integration/chroma-vector-sync.test.ts (16 tests)
Tests vector embedding synchronization with ChromaDB
- tests/utils/tag-stripping.test.ts (27 tests)
Tests privacy tag stripping utilities for both <private> and
<meta-observation> tags
All tests use real implementations where feasible, following the
project's testing philosophy of preferring integration-style tests
over unit tests with extensive mocking.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
* context update
* docs: add comment linking DEFAULT_DATA_DIR locations
Added NOTE comment in logger.ts pointing to the canonical DEFAULT_DATA_DIR
in SettingsDefaultsManager.ts. This addresses PR reviewer feedback about
the fragility of having the default defined in two places to avoid
circular dependencies.
🤖 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 crash in waitForProcessesExit when child processes exit
- Validate spawn PID before writing to PID file
- Improve error handling for Unix process cleanup
- Enhance error handling in Windows taskkill cleanup loop
- Switch health check endpoint from /api/health to /api/readiness
Replace execAsync kill command with individual process.kill calls wrapped
in try/catch to gracefully handle processes that have already exited.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
This is a backup of all work done by the 3 Phase 1 agents:
Agent A - Command Injection Fix (Issue #354):
- Fixed command injection in BranchManager.ts
- Fixed unnecessary shell usage in bun-path.ts
- Added comprehensive security test suite
- Created SECURITY.md and SECURITY_AUDIT_REPORT.md
Agent B - Observation Persistence Fix (Issue #353):
- Added PendingMessageStore from PR #335
- Integrated persistent queue into SessionManager
- Modified SDKAgent to mark messages complete
- Updated SessionStore with pending_messages migration
- Updated worker-types.ts with new interfaces
Agent C - Batch Endpoint Verification (Issue #348):
- Created batch-observations.test.ts
- Updated worker-service.mdx documentation
Also includes:
- Documentation context files (biomimetic, windows struggles)
- Build artifacts from agent testing
This work will be re-evaluated after v7.3.0 release.
* feat: Add batch fetching for observations and update documentation
- Implemented a new endpoint for fetching multiple observations by IDs in a single request.
- Updated the DataRoutes to include a POST /api/observations/batch endpoint.
- Enhanced SKILL.md documentation to reflect changes in the search process and batch fetching capabilities.
- Increased the default limit for search results from 5 to 40 for better usability.
* feat!: Fix timeline parameter passing with SearchManager alignment
BREAKING CHANGE: Timeline MCP tools now use standardized parameter names
- anchor_id → anchor
- before → depth_before
- after → depth_after
- obs_type → type (timeline tool only)
Fixes timeline endpoint failures caused by parameter name mismatch between
MCP layer and SearchManager. Adds new SessionStore methods for fetching
prompts and session summaries by ID.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
* docs: reframe timeline parameter fix as bug fix, not breaking change
The timeline tools were completely broken due to parameter name mismatch.
There's nothing to migrate from since the old parameters never worked.
Co-authored-by: Alex Newman <thedotmack@users.noreply.github.com>
* Refactor mem-search documentation and optimize API tool definitions
- Updated SKILL.md to emphasize batch fetching for observations, clarifying usage and efficiency.
- Removed deprecated tools from mcp-server.ts and streamlined tool definitions for clarity.
- Enhanced formatting in FormattingService.ts for better output readability.
- Adjusted SearchManager.ts to improve result headers and removed unnecessary search tips from combined text.
* Refactor FormattingService and SearchManager for table-based output
- Updated FormattingService to format search results as tables, including methods for formatting observations, sessions, and user prompts.
- Removed JSON format handling from SearchManager and streamlined result formatting to consistently use table format.
- Enhanced readability and consistency in search tips and formatting logic.
- Introduced token estimation for observations and improved time formatting.
* refactor: update documentation and API references for version bump and search functionalities
* Refactor code structure for improved readability and maintainability
* chore: change default model from haiku to sonnet
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
* feat: unify timeline formatting across search and context services
Extract shared timeline formatting utilities into reusable module to align
MCP search output format with context-generator's date/file-grouped format.
Changes:
- Create src/shared/timeline-formatting.ts with reusable utilities
(parseJsonArray, formatDateTime, formatTime, formatDate, toRelativePath,
extractFirstFile, groupByDate)
- Refactor context-generator.ts to use shared utilities
- Update SearchManager.search() to use date/file grouping
- Add search-specific row formatters to FormattingService
- Fix timeline methods to extract actual file paths from metadata
instead of hardcoding 'General'
- Remove Work column from search output (kept in context output)
Result: Consistent date/file-grouped markdown formatting across both
systems while maintaining their different column requirements.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
* refactor: remove redundant legend from search output
Remove legend from search/timeline results since it's already shown
in SessionStart context. Saves ~30 tokens per search result.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
* Refactor session summary rendering to remove links
- Removed link generation for session summaries in context generation and search manager.
- Updated output formatting to exclude links while maintaining the session summary structure.
- Adjusted related components in TimelineService to ensure consistency across the application.
* fix: move skillPath declaration outside try block to fix scoping bug
The skillPath variable was declared inside the try block but referenced
in the catch block for error logging. Since const is block-scoped, this
would cause a ReferenceError when the error handler executes.
Moved skillPath declaration before the try block so it's accessible in
both try and catch scopes.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
* fix: address PR #317 code review feedback
**Critical Fixes:**
- Replace happy_path_error__with_fallback debug calls with proper logger methods in mcp-server.ts
- All HTTP API calls now use logger.debug/error for consistent logging
**Code Quality Improvements:**
- Extract 90-day recency window magic numbers to named constants
- Added RECENCY_WINDOW_DAYS and RECENCY_WINDOW_MS constants in SearchManager
**Documentation:**
- Document model cost implications of Haiku → Sonnet upgrade in CHANGELOG
- Provide clear migration path for users who want to revert to Haiku
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
* refactor: simplify CHANGELOG - remove cost documentation
Removed model cost comparison documentation per user feedback.
Kept only the technical code quality improvements.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
---------
Co-authored-by: Claude Sonnet 4.5 <noreply@anthropic.com>
Co-authored-by: claude[bot] <41898282+claude[bot]@users.noreply.github.com>
Co-authored-by: Alex Newman <thedotmack@users.noreply.github.com>
- Updated shebangs in user-message-hook.js, worker-cli.js, and worker-service.cjs to use Bun instead of Node.
- Modified build-hooks.js to generate Bun-compatible shebangs in built scripts.
- Enhanced sync-marketplace.cjs to trigger a worker restart after syncing files via an HTTP request.
- Improved worker-cli.ts to exit with appropriate status codes after executing commands.
- Added build-worker-binary.js to create a Windows executable for the worker service using Bun's compile feature.
- Updated version badge in README.md to 6.0.0
- Updated 'What's New' sections in README.md and introduction.mdx
- Highlighted major session management and transcript processing improvements
- Removed restrictive permissions from .claude/settings.json
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
* refactor: Reduce continuation prompt token usage by 95 lines
Removed redundant instructions from continuation prompt that were originally
added to mitigate a session continuity issue. That issue has since been
resolved, making these detailed instructions unnecessary on every continuation.
Changes:
- Reduced continuation prompt from ~106 lines to ~11 lines (~95 line reduction)
- Changed "User's Goal:" to "Next Prompt in Session:" (more accurate framing)
- Removed redundant WHAT TO RECORD, WHEN TO SKIP, and OUTPUT FORMAT sections
- Kept concise reminder: "Continue generating observations and progress summaries..."
- Initial prompt still contains all detailed instructions
Impact:
- Significant token savings on every continuation prompt
- Faster context injection with no loss of functionality
- Instructions remain comprehensive in initial prompt
Files modified:
- src/sdk/prompts.ts (buildContinuationPrompt function)
- plugin/scripts/worker-service.cjs (compiled output)
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
* refactor: Enhance observation and summary prompts for clarity and token efficiency
* Enhance prompt clarity and instructions in prompts.ts
- Added a reminder to think about instructions before starting work.
- Simplified the continuation prompt instruction by removing "for this ongoing session."
* feat: Enhance settings.json with permissions and deny access to sensitive files
refactor: Remove PLAN-full-observation-display.md and PR_SUMMARY.md as they are no longer needed
chore: Delete SECURITY_SUMMARY.md since it is redundant after recent changes
fix: Update worker-service.cjs to streamline observation generation instructions
cleanup: Remove src-analysis.md and src-tree.md for a cleaner codebase
refactor: Modify prompts.ts to clarify instructions for memory processing
* refactor: Remove legacy worker service implementation
* feat: Enhance summary hook to extract last assistant message and improve logging
- Added function to extract the last assistant message from the transcript.
- Updated summary hook to include last assistant message in the summary request.
- Modified SDKSession interface to store last assistant message.
- Adjusted buildSummaryPrompt to utilize last assistant message for generating summaries.
- Updated worker service and session manager to handle last assistant message in summarize requests.
- Introduced silentDebug utility for improved logging and diagnostics throughout the summary process.
* docs: Add comprehensive implementation plan for ROI metrics feature
Added detailed implementation plan covering:
- Token usage capture from Agent SDK
- Database schema changes (migration #8)
- Discovery cost tracking per observation
- Context hook display with ROI metrics
- Testing and rollout strategy
Timeline: ~20 hours over 4 days
Goal: Empirical data for YC application amendment
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
* feat: Add transcript processing scripts for analysis and formatting
- Implemented `dump-transcript-readable.ts` to generate a readable markdown dump of transcripts, excluding certain entry types.
- Created `extract-rich-context-examples.ts` to extract and showcase rich context examples from transcripts, highlighting user requests and assistant reasoning.
- Developed `format-transcript-context.ts` to format transcript context into a structured markdown format for improved observation generation.
- Added `test-transcript-parser.ts` for validating data extraction from transcript JSONL files, including statistics and error reporting.
- Introduced `transcript-to-markdown.ts` for a complete representation of transcript data in markdown format, showing all context data.
- Enhanced type definitions in `transcript.ts` to support new features and ensure type safety.
- Built `transcript-parser.ts` to handle parsing of transcript JSONL files, including error handling and data extraction methods.
* Refactor hooks and SDKAgent for improved observation handling
- Updated `new-hook.ts` to clean user prompts by stripping leading slashes for better semantic clarity.
- Enhanced `save-hook.ts` to include additional tools in the SKIP_TOOLS set, preventing unnecessary observations from certain command invocations.
- Modified `prompts.ts` to change the structure of observation prompts, emphasizing the observational role and providing a detailed XML output format for observations.
- Adjusted `SDKAgent.ts` to enforce stricter tool usage restrictions, ensuring the memory agent operates solely as an observer without any tool access.
* feat: Enhance session initialization to accept user prompts and prompt numbers
- Updated `handleSessionInit` in `worker-service.ts` to extract `userPrompt` and `promptNumber` from the request body and pass them to `initializeSession`.
- Modified `initializeSession` in `SessionManager.ts` to handle optional `currentUserPrompt` and `promptNumber` parameters.
- Added logic to update the existing session's `userPrompt` and `lastPromptNumber` if a `currentUserPrompt` is provided.
- Implemented debug logging for session initialization and updates to track user prompts and prompt numbers.
---------
Co-authored-by: Claude <noreply@anthropic.com>
New Features:
- Created scripts/generate-changelog.js to auto-generate CHANGELOG.md
- Fetches all GitHub releases and formats into Keep a Changelog format
- Added npm run changelog:generate command
Version-Bump Skill Updates:
- Added Step 10: Generate CHANGELOG to workflow
- Updated verification checklist to include CHANGELOG generation
- Updated skill description and critical rules
- Single source of truth: GitHub releases
Technical Details:
- Script fetches releases via gh CLI
- Parses release bodies and formats to markdown
- Removes duplicate headers and Claude Code footers
- Sorts releases by date (newest first)
- Generates clean, consistent changelog
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Enhancements:
- Added search skill with 10 HTTP API endpoints for memory queries
- Refactored version-bump and troubleshoot skills using progressive disclosure pattern
- Added operations/ subdirectories for detailed skill documentation
- Updated CLAUDE.md with skill-based search architecture
- Enhanced worker service with search API endpoints
- Updated CHANGELOG.md with v5.4.0 migration details
Technical changes:
- New plugin/skills/search/ directory with SKILL.md
- New .claude/skills/version-bump/operations/ (workflow.md, scenarios.md)
- New plugin/skills/troubleshoot/operations/ (common-issues.md, worker.md)
- Modified src/services/worker-service.ts (added search endpoints)
- Modified plugin/scripts/worker-service.cjs (rebuilt with search API)
- Reduced main skill files by 89% using progressive disclosure
- Token savings: ~2,250 tokens per session start
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Alex Newman