Fix/mcp reasoningbank integration #818

dshep · 2025-10-16T05:11:07Z

🔗 Unify MCP and CLI Memory Storage with ReasoningBank Integration

Fixes #812

Summary

MCP memory tools (memory_usage, memory_search) and CLI memory commands previously used separate storage
systems, preventing MCP users from accessing ReasoningBank's semantic search capabilities. This PR unifies
both interfaces to share the same storage backend with automatic ReasoningBank detection.

Problem

Before this fix:

❌ CLI commands used ReasoningBank (.swarm/memory.db) with semantic search
❌ MCP tools used separate database with no semantic search
❌ Data stored via CLI was invisible to MCP (and vice versa)
❌ memory_search MCP tool returned success but no actual results
❌ MCP users forced to use CLI via Bash workarounds

Example of broken behavior:

# Store via CLI - goes to ReasoningBank
$ claude-flow memory store "auth-pattern" "Use JWT with RS256"
✅ Stored successfully in ReasoningBank

# Try to retrieve via MCP - different database!
await mcp__claude_flow__memory_usage({
  action: "retrieve",
  key: "auth-pattern"
});
// ❌ Returns: { found: false, value: null }

Solution: UnifiedMemoryManager

Created a unified memory layer that both CLI and MCP use:

Priority-based Storage System:
1. 🧠 ReasoningBank (.swarm/memory.db) - AI-powered semantic search
2. 🗄️ SQLite (unified-memory.db) - Fast SQL queries
3. 📄 JSON (memory-store.json) - Always-available fallback

Features:
- ✅ Auto-Detection: Checks for .swarm/memory.db existence
- ✅ Lazy Loading: Imports ReasoningBank adapter only when needed
- ✅ Graceful Fallback: Falls back to JSON if ReasoningBank unavailable
- ✅ Semantic Search: Query by meaning, not keywords
- ✅ Similarity Scores: Ranked results (0-100%)

Changes

1. Core Integration (src/memory/unified-memory-manager.js)

- Added ReasoningBank detection and integration
- Implemented priority-based storage selection
- Enhanced methods: store(), query(), get(), getStats()

2. MCP Server (src/mcp/mcp-server.js)

- Replaced fallback-store with UnifiedMemoryManager
- Added memory_search case statement (was missing!)
- Enhanced responses with storage_type and semantic_search metadata


Test Results ✅

CLI → MCP Interoperability (Semantic Search):
# Store via CLI
$ claude-flow memory store "authentication-best-practices" \
    "Always use environment variables for API keys..." \
    --namespace security
✅ Stored in ReasoningBank

# Query via MCP with DIFFERENT words
await memoryManager.query("How should I store API credentials?");

# Result: Found with 31.0% similarity! ✨
{
  key: "authentication-best-practices",
  score: 0.310,
  confidence: 0.80,
  mode: "reasoningbank"
}

Semantic matching works:
- Query: "How should I store API credentials?"
- Found: "Always use environment variables for API keys"
- System understands: "store credentials" ≈ "environment variables"

Impact

For MCP Users:
- 🧠 Semantic search now accessible via MCP tools
- 📊 Similarity scores in search results
- 🔄 Can read data stored via CLI
- ⚡ Auto-detection, no config needed
- 🛡️ Graceful fallback to JSON mode

For CLI Users:
- 🔗 Data now accessible via MCP tools
- ✅ No breaking changes
- 📈 Enhanced MCP response metadata

Backward Compatibility ✅

- 100% Compatible: No breaking changes to existing APIs
- JSON Fallback: Works without ReasoningBank
- Existing Data: All previous data remains accessible
- Same Signatures: No changes to MCP tool parameters

Files Changed

- src/memory/unified-memory-manager.js - ReasoningBank integration
- src/mcp/mcp-server.js - UnifiedMemoryManager adoption + missing case fix


Testing

# 1. Store via CLI
./bin/claude-flow memory store "test-key" "semantic test value" --namespace test

# 2. Query via MCP with different words
# UnifiedMemoryManager returns results with similarity scores

# 3. Verify storage type
./bin/claude-flow memory mode
# Should show: "ReasoningBank Mode: Initialized ✅"

---
Ready for review! 🎉 Full interoperability between CLI and MCP memory interfaces with semantic search
capabilities.

dshep · 2025-10-21T01:46:27Z

the PR is compatable with v2.7.0-alpha.14 - verified the issue still exists in v2.7.0-alpha.14 and this fixes it

## Merge Summary Merged upstream/main (v2.7.1) into fix/mcp-reasoningbank-integration branch. ## Conflicts Resolved ### 1. Metrics Files - Removed .claude-flow/metrics/*.json (should be gitignored) ### 2. MCP Server - neural_train API Mismatch **Problem**: Upstream v2.7.1 added neural_train code for `this.memoryStore` but this branch refactored to `this.memoryManager` **Solution**: Applied same fix as local-main: - Changed `this.memoryStore` → `this.memoryManager` (7 instances) - Fixed API calls: - `.store(key, value, {namespace, ttl, metadata})` → `.store(key, value, namespace, metadata)` - `.retrieve(key, {namespace})` → `.get(key, namespace)?.value` - `.list({namespace})` → `.query(pattern, {namespace, limit})` ## Changes from Upstream - ✅ v2.7.1 release (MCP pattern persistence) - ✅ AgentDB skills expansion - ✅ Commands migrated to skills system - ✅ Comprehensive testing suite - ✅ Docker verification infrastructure ## Neural Train Fix Adapted upstream's v2.7.1 neural_train feature to work with UnifiedMemoryManager: ```javascript // ✅ NOW WORKING: if (this.memoryManager) { await this.memoryManager.store(modelId, patternData, 'patterns', {...}); const stats = await this.memoryManager.get(statsKey, 'pattern-stats'); } ``` ## Files Changed - src/mcp/mcp-server.js (112 insertions, 112 deletions) - dist-cjs/src/mcp/mcp-server.js (rebuilt) - Removed: Old .claude/commands/** (migrated to skills) - Added: v2.7.1 test suite and documentation ## Testing ✅ Syntax validation passed ✅ Build successful ✅ Ready for PR ruvnet#818 update 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>

dshep · 2025-10-25T17:56:22Z

🔄 Updated for v2.7.1 Compatibility

This PR has been updated to resolve conflicts with upstream's v2.7.1 release.

Changes in This Update

1. Merged upstream/main (v2.7.1)

Includes all v2.7.1 features and fixes
Commands → Skills migration
Enhanced testing infrastructure
Docker verification suite

2. Fixed neural_train API Mismatch

Upstream v2.7.1 added neural_train pattern persistence using this.memoryStore, but this branch refactored to use this.memoryManager (UnifiedMemoryManager with ReasoningBank).

Applied fixes:

// ❌ Upstream v2.7.1 (doesn't work with this PR's refactoring):
if (this.memoryStore) {
  await this.memoryStore.retrieve(key, {namespace: 'patterns'});
}

// ✅ Fixed for UnifiedMemoryManager:
if (this.memoryManager) {
  const entry = await this.memoryManager.get(key, 'patterns');
  const value = entry?.value;
}

API transformations applied:

.store(key, value, {namespace, ttl, metadata}) → .store(key, value, namespace, metadata)
.retrieve(key, {namespace}) → .get(key, namespace)?.value
.list({namespace, limit}) → .query(pattern, {namespace, limit})

Files Updated

src/mcp/mcp-server.js (112 insertions, 112 deletions)
dist-cjs/src/mcp/mcp-server.js (rebuilt)

Testing

✅ Build successful
✅ Syntax validation passed
✅ Pattern persistence verified (tested on local-main)

Result

This PR now provides:

✅ ReasoningBank semantic search for MCP tools
✅ CLI-MCP data interoperability
✅ Working neural_train pattern persistence (fixed upstream bug)
✅ Compatible with v2.7.1 release
✅ All upstream tests and docs included

Ready for review! 🎉

Resolves issue #7 by integrating MCP memory tools with UnifiedMemoryManager and ReasoningBank backend, enabling semantic search for MCP users. - Added ReasoningBank detection and auto-initialization - Implemented priority-based storage: ReasoningBank → SQLite → JSON - Added semantic search routing for query operations - Updated get(), getStats(), delete(), clearNamespace() for ReasoningBank - Added storeReasoningBank() and queryReasoningBank() methods - Enhanced getStorageInfo() to report ReasoningBank capabilities - Replaced fallback-store with UnifiedMemoryManager - Updated handleMemoryUsage() to use new UnifiedMemoryManager API - Updated handleMemorySearch() for semantic search support - Fixed swarm storage operations to use unified memory - Added storage_type and semantic_search flags to responses - Comprehensive solution documentation - Test results and verification - CLI-MCP interoperability confirmation ✅ Semantic search for MCP users when ReasoningBank initialized ✅ CLI-MCP data interoperability (shared ReasoningBank backend) ✅ Auto-detection with graceful JSON fallback ✅ Storage type reporting in MCP responses ✅ 100% backward compatible - ✅ ReasoningBank detection works correctly - ✅ CLI stores data accessible via MCP - ✅ MCP stores data accessible via CLI - ✅ Semantic search returns similarity scores - ✅ Stats show correct storage type 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>

dshep · 2025-10-25T18:23:33Z

✅ PR Cleaned Up - Rebased on upstream/main

Updated approach: Rebased instead of merging to keep PR diff clean.

What Changed

Before (bad approach):

❌ Merged upstream/main INTO feature branch
❌ PR showed all v2.7.1 files as "changes" (they're already in target)
❌ Huge diff with redundant files

After (correct approach):

✅ Rebased feature branch ON TOP OF upstream/main
✅ PR now shows ONLY this PR's changes vs upstream/main
✅ Clean, focused diff

Commit Structure After Rebase

Base: upstream/main (v2.7.1) ← PR target
  ↓
329069e6 Fix: MCP memory tools now use ReasoningBank semantic search
59923aba removed md temp files  
2eff399d chore: untrack .claude-flow/metrics files
7cdd1a62 Fix: update ReasoningBank paths to use working directory
5649bf23 Fix: Adapt v2.7.1 neural_train to memoryManager API ← NEW

The Additional Fix

Added one commit to adapt upstream's v2.7.1 neural_train code to work with this PR's memoryManager refactoring.

Changes in that commit:

Changed this.memoryStore → this.memoryManager (compatibility)
Fixed API calls to use memoryManager methods
Ensures neural_train works with UnifiedMemoryManager

Result

This PR now cleanly shows:

✅ ReasoningBank integration changes
✅ UnifiedMemoryManager refactoring
✅ Semantic search for MCP tools
✅ CLI-MCP interoperability
✅ Compatible with v2.7.1 neural_train feature

No redundant v2.7.1 files - those are already in the base branch! 🎯

## Issue Upstream v2.7.1 added neural_train code using memoryStore API: ```javascript await this.memoryStore.store(key, value, {namespace, ttl, metadata}) const value = await this.memoryStore.retrieve(key, {namespace}) const list = await this.memoryStore.list({namespace, limit}) ``` This PR refactored to UnifiedMemoryManager with different API: ```javascript await this.memoryManager.store(key, value, namespace, metadata) const entry = await this.memoryManager.get(key, namespace) const list = await this.memoryManager.query(pattern, {namespace, limit}) ``` ## Solution: Backward Compatibility Layer Instead of changing upstream's neural_train code, add compatibility to UnifiedMemoryManager. ### Changes to UnifiedMemoryManager **1. Enhanced store() to accept both APIs:** ```javascript // OLD API: store(key, value, {namespace, ttl, metadata}) // NEW API: store(key, value, namespace, metadata) async store(key, value, namespaceOrOptions = 'default', metadata = {}) { // Auto-detect which API is being used if (typeof namespaceOrOptions === 'object') { // Old API - extract from options object namespace = namespaceOrOptions.namespace || 'default'; metadata = namespaceOrOptions.metadata || {}; } else { // New API - use parameters directly namespace = namespaceOrOptions; } // ... proceed with storage } ``` **2. Added retrieve() method (wraps get()):** ```javascript async retrieve(key, options = {}) { const namespace = options.namespace || 'default'; const entry = await this.get(key, namespace); return entry?.value || null; // Returns just the value } ``` **3. Added list() method (wraps query()):** ```javascript async list(options = {}) { const namespace = options.namespace || 'default'; const limit = options.limit || 100; return await this.query('', { namespace, limit }); } ``` ### Changes to MCP Server **Added memoryStore alias:** ```javascript this.memoryManager = getUnifiedMemory(); this.memoryStore = this.memoryManager; // Backward compatibility ``` ## Benefits ✅ No changes needed to upstream's neural_train code ✅ Both old and new APIs work simultaneously ✅ Clean upgrade path for future code ✅ Minimal PR footprint ## Testing ✅ Old API: store({namespace, ttl, metadata}) - WORKS ✅ Old API: retrieve({namespace}) - WORKS ✅ Old API: list({namespace, limit}) - WORKS ✅ New API: store(namespace, metadata) - WORKS (still works) ✅ Alias: this.memoryStore === this.memoryManager - WORKS ## Files Changed - src/memory/unified-memory-manager.js (3 new methods) - src/mcp/mcp-server.js (1 line: alias) - dist-cjs/* (rebuilt) 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <[email protected]>

dshep · 2025-10-25T18:31:31Z

✅ Better Solution: Backward Compatibility Layer

Changed approach to be much cleaner - instead of modifying upstream's neural_train code, I added backward compatibility to UnifiedMemoryManager.

Why This Is Better

❌ Previous approach:

Modified neural_train code to use new API
Would conflict with future upstream changes
Larger PR footprint

✅ New approach:

Added compatibility methods to UnifiedMemoryManager
Upstream's neural_train code works WITHOUT modification
Clean, minimal PR changes

Implementation

1. Enhanced store() to accept BOTH APIs:

// ✅ OLD API (what v2.7.1 uses): 
await manager.store(key, value, {namespace, ttl, metadata})

// ✅ NEW API (what this PR uses):
await manager.store(key, value, namespace, metadata)

// Auto-detects which API based on 3rd parameter type\!

2. Added retrieve() method:

async retrieve(key, {namespace}) {
  const entry = await this.get(key, namespace);
  return entry?.value || null;
}

3. Added list() method:

async list({namespace, limit}) {
  return await this.query('', {namespace, limit});
}

4. Added MCP server alias:

this.memoryManager = getUnifiedMemory();
this.memoryStore = this.memoryManager;  // Backward compatibility

Result

✅ Upstream's v2.7.1 neural_train code works unmodified
✅ Both old and new APIs supported simultaneously
✅ Minimal changes to codebase
✅ Clean upgrade path
✅ All tests pass

Testing Verified

// ✅ Old API works
await this.memoryStore.store(key, value, {namespace, metadata});
const value = await this.memoryStore.retrieve(key, {namespace});
const list = await this.memoryStore.list({namespace, limit});

// ✅ New API works
await this.memoryManager.store(key, value, namespace, metadata);
const entry = await this.memoryManager.get(key, namespace);
const results = await this.memoryManager.query(pattern, {namespace, limit});

This is a much more elegant solution! 🎯

… upstream)

dshep · 2025-10-25T18:42:47Z

🧹 Cleaned Up PR - Removed Build Artifacts

Removed all dist-cjs/ changes from this PR. These are generated build artifacts that will be created when upstream runs their build process.

What's Left in PR

Source files only:

src/mcp/mcp-server.js - MCP server changes
src/memory/unified-memory-manager.js - Backward compatibility layer
Metrics file cleanup

No more:

❌ dist-cjs/* (build artifacts)
❌ Unnecessary generated files

Benefits

✅ Cleaner PR diff
✅ Easier to review source changes
✅ No merge conflicts with upstream builds
✅ Follows best practices (don't commit build artifacts)

The PR is now focused on source code changes only! 🎯

…ryStore API Brings in backward compatibility layer from PR ruvnet#818: - UnifiedMemoryManager now supports both old and new APIs - memoryStore alias added to MCP server - v2.7.1 neural_train code works without modification - All builds and tests passing Conflicts resolved: - Kept imports from local-main (configCommand, etc.) - Added memoryStore alias from fix branch - Accepted backward-compat methods in UnifiedMemoryManager

dshep and others added 4 commits October 25, 2025 14:18

removed md temp files

59923ab

chore: untrack .claude-flow/metrics files (already in .gitignore)

2eff399

Fix: update ReasoningBank paths to use the user's working directory

7cdd1a6

dshep force-pushed the fix/mcp-reasoningbank-integration branch from 659a7ef to 5649bf2 Compare October 25, 2025 18:22

dshep force-pushed the fix/mcp-reasoningbank-integration branch from 5649bf2 to 77efb10 Compare October 25, 2025 18:30

dshep added 2 commits October 25, 2025 14:33

chore: update dist-cjs build artifacts

395c90c

Remove dist-cjs changes from PR (build artifacts will be generated by…

8064d43

… upstream)

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dshep commented Oct 16, 2025

🔗 Unify MCP and CLI Memory Storage with ReasoningBank Integration

Summary

Problem

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dshep commented Oct 21, 2025

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dshep commented Oct 25, 2025

🔄 Updated for v2.7.1 Compatibility

Changes in This Update

Files Updated

Testing

Result

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dshep commented Oct 25, 2025

✅ PR Cleaned Up - Rebased on upstream/main

What Changed

Commit Structure After Rebase

The Additional Fix

Result

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dshep commented Oct 25, 2025

✅ Better Solution: Backward Compatibility Layer

Why This Is Better

Implementation

Result

Testing Verified

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dshep commented Oct 25, 2025

🧹 Cleaned Up PR - Removed Build Artifacts

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