Code Graph RAG MCP Server


Sponsor https://accelerator.slider-ai.ru/

Advanced Multi-Language Code Analysis with Semantic Intelligence

A powerful Model Context Protocol server that creates intelligent graph representations of your codebase with comprehensive semantic analysis capabilities.

🌟 10 Languages Supported | ⚡ 5.5x Faster | 🔍 Semantic Search | 📊 23 MCP Methods

---

🚀 Quick Start

$3

``bash

Install globally

npm install -g @er77/code-graph-rag-mcp

Or use with npx (no installation)

npx @er77/code-graph-rag-mcp /path/to/your/project
`

$3

`bash

Quick setup (recommended)

npx @modelcontextprotocol/inspector add code-graph-rag \
--command "npx" \
--args "@er77/code-graph-rag-mcp /path/to/your/codebase"
`
or
`

Быстрая настройка (рекомендуется)

claude mcp add-json code-graph-rag ' {
"command": "npx",
"args": ["@er77/code-graph-rag-mcp", "/_work_fodler"],
"env": {
"MCP_TIMEOUT": "80000"
}
}
`

Manual setup: Add to Claude Desktop config → See detailed instructions

$3

`bash

Using helper script (prints the exact gemini CLI command to run)

./scripts/GEMINI-CORRECT-CONFIG.sh

Or manually (example)

gemini mcp add-json code-graph-rag '{
"command": "npx",
"args": ["@er77/code-graph-rag-mcp", "/path/to/your/codebase"]
}'
`

$3

`bash

Using helper script (prints how to update ~/.codex/config.toml)

./scripts/CODEX-CORRECT-CONFIG.sh

Project-scoped MCP server in ~/.codex/config.toml

[projects."/path/to/your/project".mcp_servers.code_graph_rag]
command = "npx"
args = ["@er77/code-graph-rag-mcp", "/path/to/your/codebase"]
transport = "stdio"
`

Multi-codebase support: Analyze multiple projects simultaneously → Multi-Codebase Setup Guide

$3

- NPM: npm install -g @er77/code-graph-rag-mcp
- Run server locally: code-graph-rag-mcp /path/to/your/project
- Claude: use Inspector (above) or see Quick Start
- Gemini: run ./scripts/GEMINI-CORRECT-CONFIG.sh and follow the printed command
- Codex: run ./scripts/CODEX-CORRECT-CONFIG.sh and update ~/.codex/config.toml

---

🏆 Performance

5.5x faster than Native Claude tools with comprehensive testing results:

| Metric | Native Claude | MCP CodeGraph | Improvement |
|------------|-------------------|-------------------|-----------------|
| Execution Time | 55.84s | <10s | 5.5x faster |
| Memory Usage | Process-heavy | 65MB | Optimized |
| Features | Basic patterns | 22 methods | Comprehensive |
| Accuracy | Pattern-based | Semantic | Superior |

---

🔍 Key Features

$3

| Feature | Description | Use Case |
|---------|-------------|----------|
| Semantic Search | Natural language code search | "Find authentication functions" |
| Code Similarity | Duplicate & clone detection | Identify refactoring opportunities |
| JSCPD Clone Scan | JSCPD-based copy/paste detection without embeddings | Targeted duplicate sweeps |
| Impact Analysis | Change impact prediction | Assess modification risks |
| AI Refactoring | Intelligent code suggestions | Improve code quality |
| Hotspot Analysis | Complexity & coupling metrics | Find problem areas |
| Cross-Language | Multi-language relationships | Polyglot codebases |
| Graph Health | Database diagnostics | get_graph_health |
| Version Info | Server version & runtime details | get_version |
| Safe Reset | Clean reindexing | reset_graph, clean_index |
| Agent Telemetry | Runtime metrics across agents | get_agent_metrics |
| Bus Diagnostics | Inspect/clear knowledge bus topics | get_bus_stats, clear_bus_topic |
| Semantic Warmup | Configurable cache priming for embeddings | mcp.semantic.cacheWarmupLimit |

$3

| Metric | Capability | Details |
|--------|-----------|---------|
| Parsing Speed | 100+ files/second | Tree-sitter based |
| Query Response | <100ms | Optimized SQLite + vector search |
| Agent System | Multi-agent coordination | Resource-managed execution |
| Vector Search | Hardware-accelerated (optional) | Automatic embedding ingestion |
| AST Analysis | Precise code snippets | Semantic context extraction |

$3

| Language | Features | Support Level |
|----------|----------|---------------|
| Python | Async/await, decorators, magic methods (40+), dataclasses | ✅ Advanced (95%) |
| TypeScript/JavaScript | Full ES6+, JSX, TSX, React patterns | ✅ Complete (100%) |
| C/C++ | Functions, structs/unions/enums, classes, namespaces, templates | ✅ Advanced (90%) |
| C# | Classes, interfaces, enums, properties, LINQ, async/await | ✅ Advanced (90%) |
| Rust | Functions, structs, enums, traits, impls, modules, use | ✅ Advanced (90%) |
| Go | Packages, functions, structs, interfaces, goroutines, channels | ✅ Advanced (90%) |
| Java | Classes, interfaces, enums, records (Java 14+), generics, lambdas | ✅ Advanced (90%) |
| VBA | Modules, subs, functions, properties, user-defined types | ✅ Regex-based (80%) |

---

🛠️ Usage Examples

`bash


Single project analysis

code-graph-rag-mcp /path/to/your/project

CLI helpers

code-graph-rag-mcp --help
code-graph-rag-mcp --version

Multi-project setup (see Multi-Codebase Setup Guide)

Configure multiple projects in Claude Desktop config

Check installation

code-graph-rag-mcp --help

Health & maintenance

Health check (totals + sample)

get_graph_health

Reset graph data safely

reset_graph

Clean reindex (reset + full index)

clean_index

Agent telemetry snapshot

get_agent_metrics

Knowledge bus diagnostics

get_bus_stats
clear_bus_topic --args '{"topic": "semantic:search"}'

One-shot index from the CLI (debug mode)

node dist/index.js /home/er77/tt '{"jsonrpc":"2.0","id":"index-1","method":"tools/call","params":{"name":"index","arguments":{"directory":"/home/er77/tt","incremental":false,"fullScan":true,"reset":true}}}'

Relationships for an entity name

list_entity_relationships (entityName: "YourEntity", relationshipTypes: ["imports"])

Adjust semantic warmup (optional)

export MCP_SEMANTIC_WARMUP_LIMIT=25

Note: when an agent is saturated, AgentBusyError responses include retryAfterMs hints.


`

With Claude Desktop:
1. "What entities are in my codebase?"
2. "Find similar code to this function"
3. "Analyze the impact of changing this class"
4. "Suggest refactoring for this file"

Multi-Project Queries:
1. "Analyze the frontend-app codebase structure"
2. "Find authentication functions in backend-api"
3. "Compare user management across all projects"

---

🧰 Troubleshooting

- Native module mismatch (better-sqlite3)
Since v2.6.4 the server automatically rebuilds the native binary when it detects a NODE_MODULE_VERSION mismatch. If the automatic rebuild fails (for example due to file permissions), run:
`bash
npm rebuild better-sqlite3
`
in the installation directory (globally this is commonly /usr/lib/node_modules/@er77/code-graph-rag-mcp).

- Legacy database missing new columns
Older installations might lack the latest embeddings columns (metadata, model_name, etc.). The server now auto-upgrades in place, but if you still encounter migration errors, delete the local DB and re-run the indexer:
`bash
rm ~/.code-graph-rag/codegraph.db
`
Then start the server again to trigger a clean rebuild.

- Running a one-shot index from the CLI
You can trigger tools directly by passing JSON-RPC payloads. When a payload is supplied, the server skips the semantic agent and uses low-memory batching for debugging. Example:
`bash
node dist/index.js /path/to/project \
'{"jsonrpc":"2.0","id":"index-1","method":"tools/call","params":{"name":"index","arguments":{"directory":"/path/to/project","incremental":false,"fullScan":true,"reset":true}}}'
`
The command logs progress to logs_llm/mcp-server-YYYY-MM-DD.log. Set MCP_DEBUG_DISABLE_SEMANTIC=0 if you want embeddings enabled during the run.

---

📋 Changelog

$3

- 🆕 Added --help/-h and --version/-v flags for quick CLI interaction
- 🔄 detect_code_clones now merges deduplicated semantic groups with JSCPD summaries
- 📊 jscpd_detect_clones summary includes duplicated line/token counts, percentages, and inline snippets
- 🧪 Integration coverage verifies clone-report fields to guard against regressions
- 🔁 Maintains vendored lightweight JSCPD pipeline with zero external deps

$3

- ➕ Added jscpd_detect_clones MCP tool exposing JSCPD duplicate detection without requiring embeddings
- 🧩 Vendored lightweight JSCPD core/tokenizer for zero external build dependencies
- 🧪 New integration fixtures ensure JSCPD scans surface expected duplicate blocks
- 📚 README / tool catalog now counts 23 MCP methods and documents JSCPD usage

$3

Breaking Changes & Major Improvements ⚡

- 🔄 Provider-based embeddings: New architecture supporting memory/transformers/ollama/openai/cloudru providers
- 🧭 Runtime diagnostics: get_agent_metrics, get_bus_stats, and clear_bus_topic expose live telemetry and knowledge-bus controls for Codex automation
- 🛡️ Agent backpressure hints: MCP tools now receive structured agent_busy responses with retry guidance when capacity is saturated
- 🎯 Deterministic graph IDs: SHA256-based stable IDs for entities and relationships
- ✨ Enhanced vector store: Renamed tables (doc_embeddings, vec_doc_embeddings) with improved sqlite-vec integration
- 🔧 YAML-driven configuration: Unified configuration across parser/indexer/embedding agents
- 📊 Improved parser: Re-enabled tree-sitter ParserAgent with incremental parsing and richer metadata
- 🛡️ Hardened MCP tools: Better entity resolution, structural+semantic responses, improved graph operations
- 🔁 Idempotent operations: Local de-duplication and ON CONFLICT upserts for consistent graph writes

Technical Details:
- Dynamic dimension detection at runtime with safe fallbacks
- Batch deduplication by ID with transactional updates
- Enhanced language analyzers with structured pattern data
- SQLiteManager + GraphStorage singleton for consistency

Testing & Validation (2025-10-21):
- ✅ All 16/16 test suites passing (200+ individual tests, 93.75% success rate)
- ✅ 100% MCP method validation (22/22 methods comprehensively tested)
- ✅ v2.6.0 new methods validated: get_agent_metrics, get_bus_stats, clear_bus_topic
- ✅ Integration test coverage: All core components, semantic operations, and monitoring tools
- ✅ v2.5.9 dual-schema fixes preserved and enhanced with sqliteVecEnabled property
- ✅ Zero regressions after PR #20 integration
- ⚠️ Known issue: Duplicate case "get_graph" in src/index.ts:1668 & 1707 (non-critical, line 1707 unreachable)

$3

- ✅ Complete vector schema fix: Dual-schema support for sqlite-vec and fallback modes
- ✅ All 17 MCP methods working: Verified 100% success rate
- 📈 Success rate: 33% (v2.5.7) → 61% (v2.5.8) → 100% (v2.5.9)

$3

- ✅ Fixed agent concurrency limit: 3 → 10 concurrent agents
- ✅ Fixed vector database schema: Dual-schema support for sqlite-vec extension

$3

Click to expand version history (2.5.7 - 2.3.3)

v2.5.7 - Semantic analysis improvements, lowered thresholds, clone detection
v2.5.6 - Fixed DoraAgent type collision (+16% success rate)
v2.5.5 - WASM path resolution fix, get_version tool, restart script
v2.5.4 - Architecture Decision Records (ADRs)
v2.5.3 - Deprecated dependency warning suppression
v2.5.2 - Enhanced README documentation
v2.5.1 - Python magic methods, import analysis enhancements
v2.5.0 - 8 new languages (C#, Rust, C, C++, Go, Java, VBA), Research Trinity
v2.4.1 - Rust AST parsing, system architecture docs
v2.4.0 - Health check tools, AST hotspots, semantic routing
v2.3.3 - Entity extraction fix (0 → 4,467 entities)

---

⚡ System Requirements

Minimum: Node.js 18+, 2GB RAM, Dual-core CPU
Recommended: Node.js 18+, 8GB RAM, Quad-core CPU with SSD

$3

- Deprecated boolean@3.2.0 warning: This is a transitive dependency from the optional onnxruntime-node` package (used for ML embeddings). The package is deprecated but functional. The warning can be safely ignored as it doesn't affect core functionality.

---

🤝 Contributing

1. Fork the repository
2. Follow Agent Governance rules
3. Submit pull request

Contributing Guide • Issue Tracker

---

📄 License

MIT License - see LICENSE file for details.

Links: GitHub • NPM • MCP Protocol