RepoGraph-Honest MCP Server

A lightweight Model Context Protocol (MCP) server that catches code hallucinations in real time — undefined symbols, wrong library API calls, dead code, and obvious type mismatches — by verifying generated code against your project structure and installed dependencies.

RepoGraph-Honest is a self-contained extraction of the "honest action routing" idea. Instead of trusting a code model blindly, it checks the symbols and APIs the model emits before they reach your editor.

It is not a heavyweight ML system: it needs only mcp, tree-sitter, and tree-sitter-python — no torch / transformers.

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Table of contents

• Features
• Installation
• Running the server
• Connecting to an MCP client
• Tool reference
• Typical workflow
• Architecture
• Development
• Sandbox security
• Contributing
• License

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Features

Capability	Tool	What it does
Project indexing	index_project	Builds a symbol index (functions / classes / variables) from a directory; caches results across calls
Dependency APIs	load_project_deps	Loads public API signatures from requirements.txt / pyproject.toml
Symbol check	check_symbol	Verifies an identifier is defined in the project
API check	check_api	Verifies a library API call is correct (e.g. pd.read_exel → suggestions)
Sandbox exec	execute_code	Runs code in a subprocess sandbox; returns stdout/stderr + error type
File scan	scan_file	Scans a whole file for undefined calls
Package APIs	load_package_apis	Loads/caches API signatures for one package
Stats	get_project_stats	Index statistics
Type check	validate_types	Lightweight AST-based structural checks (None iteration, wrong arg counts, etc.)
Dead code	find_dead_code	Finds symbols that appear unused; supports entrypoints and ignore patterns
Similar code	find_similar_code	Finds function-level code clones across the project
Call graph	explore_call_graph	Explores callers and callees of a symbol
Search	search_code	Regex search across project source files
Tool routing	choose_tool	Maps a natural-language query to the best tool

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Installation

# from source
git clone https://github.com/Fengrru/repograph-honest-mcp.git
cd repograph-honest-mcp
pip install -e .

# or just the runtime deps
pip install -r requirements.txt

Python ≥ 3.10 is required.

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Running the server

# as a module (stdio transport — what MCP clients expect)
python -m repograph_honest.mcp.server

# via the launcher script
python scripts/run_mcp_server.py

# HTTP/SSE transport (optional)
python scripts/run_mcp_server.py --transport sse --host 127.0.0.1 --port 8000

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Connecting to an MCP client

Add this to your client's MCP configuration (Cursor, Claude Desktop, VS Code, etc.):

{
  "mcpServers": {
    "repograph-honest": {
      "command": "python",
      "args": ["-m", "repograph_honest.mcp.server"],
      "cwd": "/absolute/path/to/repograph-honest-mcp"
    }
  }
}

After restarting the client, the tools above become available.

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Tool reference

All tools are exposed by the MCP server. They can also be called directly from Python (see examples/).

index_project(root_path: str, force_rebuild: bool = False) -> dict

Build (or reuse) the project symbol index.

index_project("/path/to/project")
# => {"success": True, "symbols_indexed": 42, "root": "...", "cached": False}

load_project_deps(root_path: str) -> dict

Parse requirements.txt or pyproject.toml and load the public API signatures of listed packages.

load_project_deps("/path/to/project")
# => {"success": True, "packages_loaded": ["requests", "pytest"], "total_apis": 1204}

check_symbol(symbol_name: str, file_path: str | None = None) -> dict

Check whether a symbol is defined in the indexed project.

Symbols are stored with their full module-qualified name, e.g. pkg.core.main.

check_symbol("pkg.core.main")
# => {"success": True, "symbol": "pkg.core.main", "defined": True, "location": {...}}

check_api(api_name: str) -> dict

Check whether a library API exists and get suggestions for typos.

check_api("math.sqrt")   # valid
check_api("math.sqrtt")  # invalid + suggestions

execute_code(code: str, prelude: str = "", known_names: list[str] | None = None) -> dict

Run code in a fresh subprocess with a temporary working directory and timeout.

execute_code("print(1 + 1)")
# => {"success": True, "output": "2", ...}

scan_file(file_path: str) -> dict

Scan a file for undefined calls using AST analysis.

scan_file("/path/to/project/bad.py")
# => {"success": True, "issues": [{"type": "undefined_call", "name": "...", "line": 7}]}

validate_types(code: str) -> dict

Lightweight structural checks on a code snippet:

• iterating over None
• wrong argument counts for common builtins (len, sum, etc.)
• calling constant values
• string methods on non-string constants

validate_types("for x in None:\n    pass")
# => {"success": True, "issues": [{"type": "none_iteration", ...}]}

find_dead_code(entrypoints: list[str] | None, ignore_patterns: list[str] | None, include_tests: bool = True) -> dict

Find symbols that appear unused. Provide entrypoints to keep known roots alive.

find_dead_code(entrypoints=["pkg.cli.main"])
# => {"success": True, "dead_symbols": [...], "count": 3}

explore_call_graph(symbol_name: str) -> dict

Return definitions, callers, and callees of a symbol.

explore_call_graph("pkg.core.helper")
# => {"success": True, "callers": [...], "callees": [...]}

search_code(pattern: str, glob: str = "*.py") -> dict

Regex search across project source files.

search_code(r"def \w+_helper")

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Typical workflow

1. index_project on your repo root → builds the symbol table (cached).
2. load_project_deps → loads dependency APIs.
3. Ask your coding agent to generate code; before accepting, it can:
   • check_symbol("pkg.core.my_helper") → ensure it really exists,
   • check_api("pandas.read_csv") → confirm the API name,
   • execute_code(...) → actually run the snippet and surface errors,
   • find_dead_code() → detect newly orphaned code.

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Architecture

repograph-honest-mcp/
├── repograph_honest/
│   ├── mcp/            # FastMCP server + tool implementations
│   │   ├── server.py   # entry point (mcp.run)
│   │   ├── tools.py    # tool logic
│   │   └── knowledge_base.py  # installed package API cache
│   ├── honest/         # honest action routing
│   │   ├── router.py   # HonestRouter + ToolIntent routing
│   │   └── symbol_index.py    # project-wide symbol index + cache
│   ├── structure/      # tree-sitter based extraction
│   │   ├── extractor.py
│   │   └── relations.py
│   └── sandbox/        # sandboxed execution
├── scripts/
│   └── run_mcp_server.py
├── tests/
├── .github/workflows/  # CI
│   └── ci.yml
├── pyproject.toml
├── requirements.txt
└── README.md

Key design decisions:

• AST-first: call graphs and file scans use ast instead of fragile regex.
• Module-qualified symbols: the index stores pkg.module.func so cross-file references are unambiguous.
• Lazy loading + caching: dependency APIs and project indices are cached and invalidated by content hash.
• Thread-safe global state: tool state is protected by a lock so concurrent MCP requests do not race.

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Development

pip install -e ".[dev]"
pytest
ruff check repograph_honest tests scripts
ruff format repograph_honest tests scripts

See CONTRIBUTING.md for pull-request guidelines.

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Sandbox security

execute_code runs in a subprocess with timeout protection, a temporary working directory, and optional Unix resource limits. It is safe against accidental infinite loops and simple mistakes, but it is not a hardened security boundary against malicious code. For untrusted code, run inside a container or dedicated virtual machine.

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Contributing

Contributions are welcome! Please read CONTRIBUTING.md first.

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Changelog

See CHANGELOG.md.

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License

MIT