Alex Newman 2fc4153bef refactor: decompose monolithic services into modular architecture (#534)
* docs: add monolith refactor report with system breakdown

Comprehensive analysis of codebase identifying:
- 14 files over 500 lines requiring refactoring
- 3 critical monoliths (SessionStore, SearchManager, worker-service)
- 80% code duplication across agent files
- 5-phase refactoring roadmap with domain-based architecture

* fix: prevent memory_session_id from equaling content_session_id

The bug: memory_session_id was initialized to contentSessionId as a
"placeholder for FK purposes". This caused the SDK resume logic to
inject memory agent messages into the USER's Claude Code transcript,
corrupting their conversation history.

Root cause:
- SessionStore.createSDKSession initialized memory_session_id = contentSessionId
- SDKAgent checked memorySessionId !== contentSessionId but this check
  only worked if the session was fetched fresh from DB

The fix:
- SessionStore: Initialize memory_session_id as NULL, not contentSessionId
- SDKAgent: Simple truthy check !!session.memorySessionId (NULL = fresh start)
- Database migration: Ran UPDATE to set memory_session_id = NULL for 1807
  existing sessions that had the bug

Also adds [ALIGNMENT] logging across the session lifecycle to help debug
session continuity issues:
- Hook entry: contentSessionId + promptNumber
- DB lookup: contentSessionId → memorySessionId mapping proof
- Resume decision: shows which memorySessionId will be used for resume
- Capture: logs when memorySessionId is captured from first SDK response

UI: Added "Alignment" quick filter button in LogsModal to show only
alignment logs for debugging session continuity.

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

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* refactor: improve error handling in worker-service.ts

- Fix GENERIC_CATCH anti-patterns by logging full error objects instead of just messages
- Add [ANTI-PATTERN IGNORED] markers for legitimate cases (cleanup, hot paths)
- Simplify error handling comments to be more concise
- Improve httpShutdown() error discrimination for ECONNREFUSED
- Reduce LARGE_TRY_BLOCK issues in initialization code

Part of anti-pattern cleanup plan (132 total issues)

* refactor: improve error logging in SearchManager.ts

- Pass full error objects to logger instead of just error.message
- Fixes PARTIAL_ERROR_LOGGING anti-patterns (10 instances)
- Better debugging visibility when Chroma queries fail

Part of anti-pattern cleanup (133 remaining)

* refactor: improve error logging across SessionStore and mcp-server

- SessionStore.ts: Fix error logging in column rename utility
- mcp-server.ts: Log full error objects instead of just error.message
- Improve error handling in Worker API calls and tool execution

Part of anti-pattern cleanup (133 remaining)

* Refactor hooks to streamline error handling and loading states

- Simplified error handling in useContextPreview by removing try-catch and directly checking response status.
- Refactored usePagination to eliminate try-catch, improving readability and maintaining error handling through response checks.
- Cleaned up useSSE by removing unnecessary try-catch around JSON parsing, ensuring clarity in message handling.
- Enhanced useSettings by streamlining the saving process, removing try-catch, and directly checking the result for success.

* refactor: add error handling back to SearchManager Chroma calls

- Wrap queryChroma calls in try-catch to prevent generator crashes
- Log Chroma errors as warnings and fall back gracefully
- Fixes generator failures when Chroma has issues
- Part of anti-pattern cleanup recovery

* feat: Add generator failure investigation report and observation duplication regression report

- Created a comprehensive investigation report detailing the root cause of generator failures during anti-pattern cleanup, including the impact, investigation process, and implemented fixes.
- Documented the critical regression causing observation duplication due to race conditions in the SDK agent, outlining symptoms, root cause analysis, and proposed fixes.

* fix: address PR #528 review comments - atomic cleanup and detector improvements

This commit addresses critical review feedback from PR #528:

## 1. Atomic Message Cleanup (Fix Race Condition)

**Problem**: SessionRoutes.ts generator error handler had race condition
- Queried messages then marked failed in loop
- If crash during loop → partial marking → inconsistent state

**Solution**:
- Added `markSessionMessagesFailed()` to PendingMessageStore.ts
- Single atomic UPDATE statement replaces loop
- Follows existing pattern from `resetProcessingToPending()`

**Files**:
- src/services/sqlite/PendingMessageStore.ts (new method)
- src/services/worker/http/routes/SessionRoutes.ts (use new method)

## 2. Anti-Pattern Detector Improvements

**Problem**: Detector didn't recognize logger.failure() method
- Lines 212 & 335 already included "failure"
- Lines 112-113 (PARTIAL_ERROR_LOGGING detection) did not

**Solution**: Updated regex patterns to include "failure" for consistency

**Files**:
- scripts/anti-pattern-test/detect-error-handling-antipatterns.ts

## 3. Documentation

**PR Comment**: Added clarification on memory_session_id fix location
- Points to SessionStore.ts:1155
- Explains why NULL initialization prevents message injection bug

## Review Response

Addresses "Must Address Before Merge" items from review:
 Clarified memory_session_id bug fix location (via PR comment)
 Made generator error handler message cleanup atomic
 Deferred comprehensive test suite to follow-up PR (keeps PR focused)

## Testing

- Build passes with no errors
- Anti-pattern detector runs successfully
- Atomic cleanup follows proven pattern from existing methods

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

Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>

* fix: FOREIGN KEY constraint and missing failed_at_epoch column

Two critical bugs fixed:

1. Missing failed_at_epoch column in pending_messages table
   - Added migration 20 to create the column
   - Fixes error when trying to mark messages as failed

2. FOREIGN KEY constraint failed when storing observations
   - All three agents (SDK, Gemini, OpenRouter) were passing
     session.contentSessionId instead of session.memorySessionId
   - storeObservationsAndMarkComplete expects memorySessionId
   - Added null check and clear error message

However, observations still not saving - see investigation report.

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

Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>

* Refactor hook input parsing to improve error handling

- Added a nested try-catch block in new-hook.ts, save-hook.ts, and summary-hook.ts to handle JSON parsing errors more gracefully.
- Replaced direct error throwing with logging of the error details using logger.error.
- Ensured that the process exits cleanly after handling input in all three hooks.

* docs: update monolith report post session-logging merge

- SessionStore grew to 2,011 lines (49 methods) - highest priority
- SearchManager reduced to 1,778 lines (improved)
- Agent files reduced by ~45 lines combined
- Added trend indicators and post-merge observations
- Core refactoring proposal remains valid

* refactor(sqlite): decompose SessionStore into modular architecture

Extract the 2011-line SessionStore.ts monolith into focused, single-responsibility
modules following grep-optimized progressive disclosure pattern:

New module structure:
- sessions/ - Session creation and retrieval (create.ts, get.ts, types.ts)
- observations/ - Observation storage and queries (store.ts, get.ts, recent.ts, files.ts, types.ts)
- summaries/ - Summary storage and queries (store.ts, get.ts, recent.ts, types.ts)
- prompts/ - User prompt management (store.ts, get.ts, types.ts)
- timeline/ - Cross-entity timeline queries (queries.ts)
- import/ - Bulk import operations (bulk.ts)
- migrations/ - Database migrations (runner.ts)

New coordinator files:
- Database.ts - ClaudeMemDatabase class with re-exports
- transactions.ts - Atomic cross-entity transactions
- Named re-export facades (Sessions.ts, Observations.ts, etc.)

Key design decisions:
- All functions take `db: Database` as first parameter (functional style)
- Named re-exports instead of index.ts for grep-friendliness
- SessionStore retained as backward-compatible wrapper
- Target file size: 50-150 lines (60% compliance)

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

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* refactor(agents): extract shared logic into modular architecture

Consolidate duplicate code across SDKAgent, GeminiAgent, and OpenRouterAgent
into focused utility modules. Total reduction: 500 lines (29%).

New modules in src/services/worker/agents/:
- ResponseProcessor.ts: Atomic DB transactions, Chroma sync, SSE broadcast
- ObservationBroadcaster.ts: SSE event formatting and dispatch
- SessionCleanupHelper.ts: Session state cleanup and stuck message reset
- FallbackErrorHandler.ts: Provider error detection for fallback logic
- types.ts: Shared interfaces (WorkerRef, SSE payloads, StorageResult)

Bug fix: SDKAgent was incorrectly using obs.files instead of obs.files_read
and hardcoding files_modified to empty array.

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

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* refactor(search): extract search strategies into modular architecture

Decompose SearchManager into focused strategy pattern with:
- SearchOrchestrator: Coordinates strategy selection and fallback
- ChromaSearchStrategy: Vector semantic search via ChromaDB
- SQLiteSearchStrategy: Filter-only queries for date/project/type
- HybridSearchStrategy: Metadata filtering + semantic ranking
- ResultFormatter: Markdown table formatting for results
- TimelineBuilder: Chronological timeline construction
- Filter modules: DateFilter, ProjectFilter, TypeFilter

SearchManager now delegates to new infrastructure while maintaining
full backward compatibility with existing public API.

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

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* refactor(context): decompose context-generator into modular architecture

Extract 660-line monolith into focused components:
- ContextBuilder: Main orchestrator (~160 lines)
- ContextConfigLoader: Configuration loading
- TokenCalculator: Token budget calculations
- ObservationCompiler: Data retrieval and query building
- MarkdownFormatter/ColorFormatter: Output formatting
- Section renderers: Header, Timeline, Summary, Footer

Maintains full backward compatibility - context-generator.ts now
delegates to new ContextBuilder while preserving public API.

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

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* refactor(worker): decompose worker-service into modular infrastructure

Split 2000+ line monolith into focused modules:

Infrastructure:
- ProcessManager: PID files, signal handlers, child process cleanup
- HealthMonitor: Port checks, health polling, version matching
- GracefulShutdown: Coordinated cleanup on exit

Server:
- Server: Express app setup, core routes, route registration
- Middleware: Re-exports from existing middleware
- ErrorHandler: Centralized error handling with AppError class

Integrations:
- CursorHooksInstaller: Full Cursor IDE integration (registry, hooks, MCP)

WorkerService now acts as thin coordinator wiring all components together.
Maintains full backward compatibility with existing public API.

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

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* Refactor session queue processing and database interactions

- Implement claim-and-delete pattern in SessionQueueProcessor to simplify message handling and eliminate duplicate processing.
- Update PendingMessageStore to support atomic claim-and-delete operations, removing the need for intermediate processing states.
- Introduce storeObservations method in SessionStore for simplified observation and summary storage without message tracking.
- Remove deprecated methods and clean up session state management in worker agents.
- Adjust response processing to accommodate new storage patterns, ensuring atomic transactions for observations and summaries.
- Remove unnecessary reset logic for stuck messages due to the new queue handling approach.

* Add duplicate observation cleanup script

Script to clean up duplicate observations created by the batching bug
where observations were stored once per message ID instead of once per
observation. Includes safety checks to always keep at least one copy.

Usage:
  bun scripts/cleanup-duplicates.ts           # Dry run
  bun scripts/cleanup-duplicates.ts --execute # Delete duplicates
  bun scripts/cleanup-duplicates.ts --aggressive # Ignore time window

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

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

---------

Co-authored-by: Claude <noreply@anthropic.com>
2026-01-03 21:22:27 -05:00
2025-10-03 18:20:47 -04:00
2026-01-03 18:57:27 -05:00


Claude-Mem

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Persistent memory compression system built for Claude Code.

License Version Node Mentioned in Awesome Claude Code

thedotmack/claude-mem | Trendshift


Claude-Mem Preview

Quick StartHow It WorksSearch ToolsDocumentationConfigurationTroubleshootingLicense

Claude-Mem seamlessly preserves context across sessions by automatically capturing tool usage observations, generating semantic summaries, and making them available to future sessions. This enables Claude to maintain continuity of knowledge about projects even after sessions end or reconnect.


Quick Start

Start a new Claude Code session in the terminal and enter the following commands:

> /plugin marketplace add thedotmack/claude-mem

> /plugin install claude-mem

Restart Claude Code. Context from previous sessions will automatically appear in new sessions.

Key Features:

  • 🧠 Persistent Memory - Context survives across sessions
  • 📊 Progressive Disclosure - Layered memory retrieval with token cost visibility
  • 🔍 Skill-Based Search - Query your project history with mem-search skill
  • 🖥️ Web Viewer UI - Real-time memory stream at http://localhost:37777
  • 💻 Claude Desktop Skill - Search memory from Claude Desktop conversations
  • 🔒 Privacy Control - Use <private> tags to exclude sensitive content from storage
  • ⚙️ Context Configuration - Fine-grained control over what context gets injected
  • 🤖 Automatic Operation - No manual intervention required
  • 🔗 Citations - Reference past observations with IDs (access via http://localhost:37777/api/observation/{id} or view all in the web viewer at http://localhost:37777)
  • 🧪 Beta Channel - Try experimental features like Endless Mode via version switching

Documentation

📚 View Full Documentation - Browse markdown docs on GitHub

Getting Started

Best Practices

Architecture

Configuration & Development


How It Works

Core Components:

  1. 5 Lifecycle Hooks - SessionStart, UserPromptSubmit, PostToolUse, Stop, SessionEnd (6 hook scripts)
  2. Smart Install - Cached dependency checker (pre-hook script, not a lifecycle hook)
  3. Worker Service - HTTP API on port 37777 with web viewer UI and 10 search endpoints, managed by Bun
  4. SQLite Database - Stores sessions, observations, summaries
  5. mem-search Skill - Natural language queries with progressive disclosure
  6. Chroma Vector Database - Hybrid semantic + keyword search for intelligent context retrieval

See Architecture Overview for details.


MCP Search Tools

Claude-Mem provides intelligent memory search through 4 MCP tools following a token-efficient 3-layer workflow pattern:

The 3-Layer Workflow:

  1. search - Get compact index with IDs (~50-100 tokens/result)
  2. timeline - Get chronological context around interesting results
  3. get_observations - Fetch full details ONLY for filtered IDs (~500-1,000 tokens/result)

How It Works:

  • Claude uses MCP tools to search your memory
  • Start with search to get an index of results
  • Use timeline to see what was happening around specific observations
  • Use get_observations to fetch full details for relevant IDs
  • ~10x token savings by filtering before fetching details

Available MCP Tools:

  1. search - Search memory index with full-text queries, filters by type/date/project
  2. timeline - Get chronological context around a specific observation or query
  3. get_observations - Fetch full observation details by IDs (always batch multiple IDs)
  4. __IMPORTANT - Workflow documentation (always visible to Claude)

Example Usage:

// Step 1: Search for index
search(query="authentication bug", type="bugfix", limit=10)

// Step 2: Review index, identify relevant IDs (e.g., #123, #456)

// Step 3: Fetch full details
get_observations(ids=[123, 456])

See Search Tools Guide for detailed examples.


Beta Features

Claude-Mem offers a beta channel with experimental features like Endless Mode (biomimetic memory architecture for extended sessions). Switch between stable and beta versions from the web viewer UI at http://localhost:37777 → Settings.

See Beta Features Documentation for details on Endless Mode and how to try it.


System Requirements

  • Node.js: 18.0.0 or higher
  • Claude Code: Latest version with plugin support
  • Bun: JavaScript runtime and process manager (auto-installed if missing)
  • uv: Python package manager for vector search (auto-installed if missing)
  • SQLite 3: For persistent storage (bundled)

Configuration

Settings are managed in ~/.claude-mem/settings.json (auto-created with defaults on first run). Configure AI model, worker port, data directory, log level, and context injection settings.

See the Configuration Guide for all available settings and examples.


Development

See the Development Guide for build instructions, testing, and contribution workflow.


Troubleshooting

If experiencing issues, describe the problem to Claude and the troubleshoot skill will automatically diagnose and provide fixes.

See the Troubleshooting Guide for common issues and solutions.


Bug Reports

Create comprehensive bug reports with the automated generator:

cd ~/.claude/plugins/marketplaces/thedotmack
npm run bug-report

Contributing

Contributions are welcome! Please:

  1. Fork the repository
  2. Create a feature branch
  3. Make your changes with tests
  4. Update documentation
  5. Submit a Pull Request

See Development Guide for contribution workflow.


License

This project is licensed under the GNU Affero General Public License v3.0 (AGPL-3.0).

Copyright (C) 2025 Alex Newman (@thedotmack). All rights reserved.

See the LICENSE file for full details.

What This Means:

  • You can use, modify, and distribute this software freely
  • If you modify and deploy on a network server, you must make your source code available
  • Derivative works must also be licensed under AGPL-3.0
  • There is NO WARRANTY for this software

Note on Ragtime: The ragtime/ directory is licensed separately under the PolyForm Noncommercial License 1.0.0. See ragtime/LICENSE for details.


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