codebase-memory-mcp-pro-knowledge-graph

v2026.09.25
reason-machines/mcp-skills00

Community fork of codebase-memory-mcp with incremental-reindex fixes — pure-C knowledge-graph MCP server for AI code exploration

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Install command
npx skhub add reason-machines/codebase-memory-mcp-pro-knowledge-graph
Markdown
SKILL.md

codebase-memory-mcp-pro Knowledge Graph

Skill by ara.so — MCP Skills collection.

Overview

codebase-memory-mcp-pro is a community fork of DeusData/codebase-memory-mcp that provides a pure-C knowledge graph MCP server for AI code exploration. It indexes codebases using tree-sitter AST analysis across 158 languages, building a persistent graph of functions, classes, call chains, and cross-file references.

Key improvements in this fork:

  • Incremental-reindex correctness — preserves inbound cross-file CALLS edges; editing a file no longer orphans calls into its symbols
  • Enhanced explore tool — single-call blast-radius analysis with callers, neighbors, inline hotspot flags, and line-numbered source
  • Swift type fidelity — struct/enum/actor are distinct graph labels; enum cases extracted as EnumCase nodes
  • Cypher aggregation fix — non-aggregate functions mixed with aggregates now group correctly
  • detect_changes blast radius — depth parameter produces transitive caller impact analysis

The fork ships no prebuilt binaries — you build from source to get all integrated fixes.

Installation

Build from Source

# Clone the fork
git clone https://github.com/win4r/codebase-memory-mcp-pro.git
cd codebase-memory-mcp-pro

# Build (first build compiles 158 tree-sitter grammars — takes a few minutes)
./scripts/build.sh
# → build/c/codebase-memory-mcp (reports version: dev)

# Install to PATH
cp build/c/codebase-memory-mcp ~/.local/bin/

# Add as stdio MCP server (available in all projects)
claude mcp add codebase-memory -s user -- ~/.local/bin/codebase-memory-mcp

Iterative rebuilds (much faster after first build):

make -j -f Makefile.cbm cbm

Verify Integration

Confirm the integrated fixes are live:

# Index a repository
codebase-memory-mcp cli index_repository '{"repo_path":"/path/to/repo"}'

# Test PR #465 — node properties survive WITH aggregation
codebase-memory-mcp cli query_graph '{
  "project": "<name>",
  "query": "MATCH (a)-[:CALLS]->(b) WITH b, count(a) AS c RETURN b.file_path, c LIMIT 1"
}'
# Non-empty file_path means you're running the cherry-picked build

⚠️ Do not run codebase-memory-mcp update — it pulls upstream and overwrites the integrated build. Use ./scripts/build.sh to update instead.

Core MCP Tools

The server exposes 15 MCP tools. Key tools in this fork:

explore (Fork Enhancement)

One-call blast-radius analysis — returns callers, neighbors, and line-numbered source:

// AI agent invocation
{
  "name": "explore",
  "arguments": {
    "project": "my-project",
    "symbol_name": "processOrder",
    "include_source": true,
    "max_callers": 20,
    "max_neighbors": 10
  }
}

Returns:

  • Blast radius: attributed callers + inline fan-in hotspot flags
  • Neighbors: 1-hop callees + same-file siblings
  • Source: verbatim line-numbered code grouped by file
  • Cypher escape-hatch: optional cypher_query parameter for custom graph traversal

index_repository

Build the knowledge graph:

{
  "name": "index_repository",
  "arguments": {
    "repo_path": "/path/to/repo",
    "project_name": "my-project"  // optional, defaults to dir name
  }
}

Incremental re-index (fork fix: preserves cross-file CALLS edges):

# Edit files, then re-run index_repository
# Inbound calls to edited symbols are preserved

query_graph

Execute Cypher queries against the knowledge graph:

{
  "name": "query_graph",
  "arguments": {
    "project": "my-project",
    "query": "MATCH (f:Function)-[:CALLS]->(g:Function) WHERE f.file_path =~ '.*service.*' RETURN f.name, g.name, g.file_path LIMIT 10"
  }
}

Common patterns:

// Find all callers of a function
MATCH (caller)-[:CALLS]->(target:Function)
WHERE target.name = 'processPayment'
RETURN caller.name, caller.file_path

// Functions with most callers (hotspots)
MATCH (caller)-[:CALLS]->(target)
WITH target, count(caller) AS fan_in
WHERE fan_in > 5
RETURN target.name, target.file_path, fan_in
ORDER BY fan_in DESC

// Call chain between two symbols
MATCH path = shortestPath(
  (a:Function {name: 'handleRequest'})-[:CALLS*..10]->(b:Function {name: 'saveToDatabase'})
)
RETURN [n in nodes(path) | n.name] AS call_chain

// Dead code detection (no inbound calls)
MATCH (f:Function)
WHERE NOT ()-[:CALLS]->(f)
  AND f.visibility = 'public'
RETURN f.name, f.file_path

// Swift enum cases (fork feature)
MATCH (e:Enum)-[:CONTAINS]->(case:EnumCase)
WHERE e.name = 'AppError'
RETURN case.name, case.line_start

Fork fix: Aggregations now group correctly:

// This returns one row per edge type (not collapsed into one row)
MATCH (a)-[r]->(b)
RETURN type(r), count(*) AS edge_count

detect_changes

Detect modified files and impacted symbols:

{
  "name": "detect_changes",
  "arguments": {
    "project": "my-project",
    "since": "HEAD~5",  // fork fix: honors since parameter
    "depth": 2          // fork feature: transitive caller blast radius
  }
}

Fork enhancement: depth parameter produces transitive caller blast radius:

  • impacted_symbols includes callers up to depth hops
  • Each symbol tagged with hop (0 = changed, 1+ = caller) and transitive flag
  • impacted_count deduplicated across hops

Example response:

{
  "changed_files": ["src/payment/processor.ts"],
  "impacted_symbols": [
    {
      "name": "processPayment",
      "file_path": "src/payment/processor.ts",
      "hop": 0,
      "transitive": false
    },
    {
      "name": "handleCheckout",
      "file_path": "src/checkout/handler.ts",
      "hop": 1,
      "transitive": true
    },
    {
      "name": "completeOrder",
      "file_path": "src/order/service.ts",
      "hop": 2,
      "transitive": true
    }
  ],
  "impacted_count": 12
}

trace_path

Find call paths between two symbols:

{
  "name": "trace_path",
  "arguments": {
    "project": "my-project",
    "from_symbol": "handleRequest",
    "to_symbol": "saveToDatabase",
    "max_depth": 10
  }
}

get_code_snippet

Retrieve source code with line numbers:

{
  "name": "get_code_snippet",
  "arguments": {
    "project": "my-project",
    "file_path": "src/utils/validator.ts",
    "start_line": 45,
    "end_line": 60
  }
}

Fork fix: Returns valid UTF-8 (handles non-UTF-8 source files gracefully).

Swift Enhancements (Fork)

Distinct Type Labels

Stock upstream lumps Swift struct/enum/actor as Class. This fork emits distinct labels:

// Find all Swift structs
MATCH (s:Struct)
WHERE s.file_path =~ '.*\\.swift$'
RETURN s.name, s.file_path

// Find all actors
MATCH (a:Actor)
RETURN a.name

// Enum with cases
MATCH (e:Enum)-[:CONTAINS]->(case:EnumCase)
WHERE e.name = 'NetworkError'
RETURN case.name

Enum Case Extraction

Enum cases (including multi-name case a, b, c lines) are extracted as EnumCase nodes:

// Source
enum Status {
    case pending, processing  // Multi-name case
    case completed(Date)
    case failed(Error)
}

// Query
MATCH (e:Enum {name: 'Status'})-[:CONTAINS]->(case:EnumCase)
RETURN case.name
// Returns: pending, processing, completed, failed

Static Method Dedup Fix

Fork fix: An enum's static func is no longer double-emitted as both Method and Function nodes.

CLI Usage

The binary supports both MCP stdio mode (for agents) and direct CLI invocation:

# MCP stdio mode (agent communication)
codebase-memory-mcp

# Direct CLI tool invocation
codebase-memory-mcp cli <tool_name> '<json_args>'

# Examples
codebase-memory-mcp cli index_repository '{"repo_path": "/path/to/repo"}'

codebase-memory-mcp cli query_graph '{
  "project": "my-project",
  "query": "MATCH (f:Function) RETURN f.name LIMIT 5"
}'

codebase-memory-mcp cli explore '{
  "project": "my-project",
  "symbol_name": "parseConfig",
  "include_source": true
}'

Configuration

MCP Server Configuration

Add to ~/.config/claude/claude_desktop_config.json (or agent-specific config):

{
  "mcpServers": {
    "codebase-memory": {
      "command": "/home/user/.local/bin/codebase-memory-mcp",
      "args": [],
      "env": {}
    }
  }
}

Environment Variables

# Optional: custom database location
export CBM_DB_PATH=/path/to/custom/db

# Optional: log level (debug, info, warn, error)
export CBM_LOG_LEVEL=info

Project-Specific Configuration

Create .codebase-memory.json in repository root:

{
  "exclude_paths": [
    "node_modules",
    "vendor",
    "build",
    "dist",
    ".git",
    "*.test.ts"
  ],
  "include_extensions": [
    ".ts", ".tsx", ".js", ".jsx",
    ".py", ".go", ".rs", ".c", ".cpp", ".swift"
  ],
  "max_file_size_kb": 1024
}

Real-World Patterns

Pattern 1: Impact Analysis Before Refactoring

// 1. Find the function
const exploreResult = await explore({
  project: "my-api",
  symbol_name: "validateUser",
  include_source: true,
  max_callers: 50
});

// 2. Check blast radius
const callerCount = exploreResult.callers.length;
const hasHighFanIn = callerCount > 10;

// 3. Query transitive impact
const impactResult = await query_graph({
  project: "my-api",
  query: `
    MATCH (caller)-[:CALLS*1..3]->(target:Function)
    WHERE target.name = 'validateUser'
    RETURN DISTINCT caller.name, caller.file_path
  `
});

// 4. Make informed decision
if (hasHighFanIn) {
  // High-risk refactor: write comprehensive tests first
} else {
  // Low-risk: proceed with confidence
}

Pattern 2: Dead Code Detection

// Find public functions with no callers
const deadCode = await query_graph({
  project: "my-api",
  query: `
    MATCH (f:Function)
    WHERE NOT ()-[:CALLS]->(f)
      AND f.visibility = 'public'
      AND f.file_path =~ '.*src/.*'
    RETURN f.name, f.file_path, f.line_start
    ORDER BY f.file_path
  `
});

// Cross-reference with exports
const exports = await query_graph({
  project: "my-api",
  query: `
    MATCH (m:Module)-[:EXPORTS]->(f)
    RETURN f.name, m.file_path
  `
});

// Candidates for deletion: deadCode NOT IN exports

Pattern 3: Incremental Re-index Workflow

#!/bin/bash
# safe-refactor.sh

# 1. Index current state
codebase-memory-mcp cli index_repository '{"repo_path": "."}'

# 2. Snapshot call graph
codebase-memory-mcp cli query_graph '{
  "project": "my-api",
  "query": "MATCH (a)-[:CALLS]->(b {name: \"targetFunc\"}) RETURN a.name, a.file_path"
}' > before.json

# 3. Make changes
vim src/core/target.ts

# 4. Re-index (fork: preserves inbound CALLS edges)
codebase-memory-mcp cli index_repository '{"repo_path": "."}'

# 5. Verify call graph integrity
codebase-memory-mcp cli query_graph '{
  "project": "my-api",
  "query": "MATCH (a)-[:CALLS]->(b {name: \"targetFunc\"}) RETURN a.name, a.file_path"
}' > after.json

# 6. Compare
diff before.json after.json

Pattern 4: Architecture Documentation

// Generate module dependency graph
const modules = await query_graph({
  project: "my-api",
  query: `
    MATCH (m1:Module)-[:IMPORTS]->(m2:Module)
    RETURN m1.file_path AS from, m2.file_path AS to
  `
});

// Detect circular dependencies
const cycles = await query_graph({
  project: "my-api",
  query: `
    MATCH path = (m:Module)-[:IMPORTS*2..10]->(m)
    RETURN [n in nodes(path) | n.file_path] AS cycle
    LIMIT 10
  `
});

// Find architectural layers (no upward imports)
const layers = await query_graph({
  project: "my-api",
  query: `
    MATCH (m:Module)
    WHERE m.file_path =~ '.*/domain/.*'
      AND NOT (m)-[:IMPORTS]->(:Module {file_path: ~'.*/infrastructure/.*'})
    RETURN m.file_path AS clean_domain_module
  `
});

Troubleshooting

Issue: "No such project"

Cause: Project not indexed or wrong name.

# List indexed projects
codebase-memory-mcp cli query_graph '{
  "project": "any",
  "query": "MATCH (p:Project) RETURN p.name"
}'

# Re-index with explicit name
codebase-memory-mcp cli index_repository '{
  "repo_path": "/path/to/repo",
  "project_name": "exact-name"
}'

Issue: Incremental re-index loses edges (upstream bug)

Solution: You're running stock upstream, not the fork. Rebuild from source:

cd codebase-memory-mcp-pro
./scripts/build.sh
cp build/c/codebase-memory-mcp ~/.local/bin/

Verify integration:

codebase-memory-mcp cli query_graph '{
  "project": "test",
  "query": "MATCH (a)-[:CALLS]->(b) WITH b, count(a) AS c RETURN b.file_path, c LIMIT 1"
}'
# Non-empty file_path = fork build

Issue: Cypher query returns unexpected single row

Cause: Aggregation bug in upstream (fixed in fork).

// This should return one row per edge type
MATCH (a)-[r]->(b)
RETURN type(r), count(*)
// Upstream: collapses into single row
// Fork: groups correctly by type(r)

Rebuild from fork source if you're seeing this.

Issue: Swift enums/structs labeled as Class

Solution: Fork emits distinct labels. Query with specific types:

// Fork
MATCH (s:Struct) RETURN s.name

// Upstream workaround (not recommended)
MATCH (s:Class)
WHERE s.kind = 'struct'  // Property may not exist
RETURN s.name

Issue: Build fails on macOS with libgit2 ≥ 1.8

Solution: Already fixed in fork (PR #512 integrated). If still failing:

brew info libgit2  # Check version
# Ensure you're building from fork, not upstream
git remote -v  # Should show win4r/codebase-memory-mcp-pro
./scripts/build.sh

Issue: UTF-8 errors in get_code_snippet

Solution: Fixed in fork (PR #526). Rebuild from source.

Issue: detect_changes ignores since parameter

Solution: Fixed in fork (PR #464). Rebuild from source.

Advanced: Custom Cypher Patterns

Find HTTP Route Handlers

MATCH (route:Route)-[:HANDLED_BY]->(handler:Function)
WHERE route.method = 'POST'
RETURN route.path, handler.name, handler.file_path
ORDER BY route.path

Cross-Service Call Analysis

MATCH (caller:Function)-[:HTTP_CALL]->(route:Route)
WHERE caller.file_path =~ '.*service-a/.*'
  AND route.service = 'service-b'
RETURN caller.name, route.path, route.method

Complexity Analysis

MATCH (f:Function)
WHERE f.cyclomatic_complexity > 10
RETURN f.name, f.file_path, f.cyclomatic_complexity
ORDER BY f.cyclomatic_complexity DESC
LIMIT 20

Ownership Mapping (by directory)

MATCH (f:Function)
WITH split(f.file_path, '/')[0..3] AS module, count(f) AS function_count
RETURN module, function_count
ORDER BY function_count DESC

Integration with AI Agents

Claude Code / Cursor

// ~/.config/claude/claude_desktop_config.json
{
  "mcpServers": {
    "codebase-memory": {
      "command": "/home/user/.local/bin/codebase-memory-mcp"
    }
  }
}

Aider

# .aider.conf.yml
mcp:
  servers:
    - name: codebase-memory
      command: /home/user/.local/bin/codebase-memory-mcp

Generic MCP Client

import { MCPClient } from '@modelcontextprotocol/sdk';

const client = new MCPClient({
  command: '/home/user/.local/bin/codebase-memory-mcp',
  args: []
});

await client.connect();

const result = await client.callTool('explore', {
  project: 'my-api',
  symbol_name: 'processOrder'
});

console.log(result);

Performance Notes

  • Linux kernel (28M LOC, 75K files): 3 minutes to index
  • Average repository: milliseconds
  • Graph queries: <1ms for simple patterns, <100ms for complex traversals
  • Memory: RAM-first pipeline with LZ4 compression; memory released after indexing

Contributing to the Fork

This is a community fork tracking upstream. To contribute:

  1. Upstream PRs first: Submit fixes to DeusData/codebase-memory-mcp
  2. Fork-specific enhancements: Submit PRs to win4r/codebase-memory-mcp-pro
  3. Integration requests: Open an issue if an upstream PR should be cherry-picked into the fork

License

MIT License (unchanged from upstream). See LICENSE.

All credit for the original engine: DeusData. This fork exists to integrate fixes faster than upstream merge cycles.

Discovery
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Version
Latest version metadata

Version

v2026.09.25

Published

Sep 25, 2026

Category

Uncategorized

License

NOASSERTION

Source path

skills/codebase-memory-mcp-pro-knowledge-graph

Default branch

main

Latest commit

329e67c

Tree SHA

01fd22f