<div align="center">

HonestCode MCP Server

Catch AI code hallucinations before they reach your editor.

A lightweight Model Context Protocol (MCP) server that verifies AI-generated code against your actual project structure and installed dependencies — detecting undefined symbols, wrong API calls, dead code, and type mismatches in real time.

100% local. No data leaves your machine.

</div>

---

Contents

• Why HonestCode?
• Performance
• Quick Start
• Environment Variables
• Multi-language support (optional)
• Supported Platforms and Agents
• Tool Reference
• CLI Usage
• Library Usage
• Architecture
• When NOT to use HonestCode
• Troubleshooting
• Development
• Security
• Telemetry
• Roadmap
• Changelog
• Contributing
• License

---

Why HonestCode?

AI coding assistants hallucinate. They invent function names, fabricate library APIs, and produce dead code. HonestCode acts as a deterministic verification layer between the model and your editor — pure AST analysis, no LLM calls, no network requests.

graph LR
    A["AI Model generates code"] -->|sends code| B["HonestCode verifies against project"]
    B -->|clean code| C["Editor receives verified code"]

One tool by default: scan_file

By default the server exposes one primary tool — scan_file. Give it a Python file and it returns every undefined symbol, incorrect API call, and structural issue in a single trip.

Exposing a single tool is deliberate. Measured agent behavior shows that one well-aimed tool steers agents to a direct answer better than a menu of narrower ones — fewer mis-picks, fewer round-trips. 16 additional tools exist for power users; opt in via the HONESTCODE_TOOLS environment variable (see Environment Variables).

Key differentiators

	HonestCode	grep / Read	RAG over code
Deterministic	AST-based, reproducible	Exact string match	Embedding variance
Cross-file	Module-qualified symbols	Single-file only	Chunk-level
Type-aware	Argument counts, None iteration	No	No
Zero latency	Pre-indexed, cached	Per-query scan	Per-query embed
100% local	No network calls	No	Often requires API

---

Performance

Numbers below are measured, not estimated. Re-run them yourself:

# Local project
python scripts/benchmark.py --target /path/to/project --repeat 5
# External real-world repos (clones them into a temp dir)
python scripts/benchmark.py --repos psf/requests pallets/flask --format markdown

Measured on this repository (43 Python modules, ~7400 LOC, Python 3.14, median of 3 runs on a developer laptop, Windows):

Operation	Measured	Note
index_project (cold)	~143 ms	Content-hash cached; skips unchanged files
index_project (cached)	< 1 ms	In-memory cache hit
scan_file	~35 ms	AST parse + symbol lookup
check_api	< 1 ms	Dictionary lookup on cached API index
explore_call_graph (hot)	~1 ms	SQLite graph cache hit; cold rebuild ~278 ms
find_dead_code	~1.4 ms	Reads the persisted reference graph
find_similar_code	~3750 ms	O(n²) SequenceMatcher; dominated by pair count
search_code	~16 ms	FTS5 candidate narrowing + regex on hits

The call graph (definitions + references) is persisted to SQLite next to the symbol index, keyed by content hashes of every source file. Graph queries (explore_call_graph, find_dead_code, explore_impact, affected_files) read from disk instead of re-parsing the project on each call — the first call after a change pays the cold rebuild, every later call is a cache hit. find_similar_code uses a length-ratio pre-filter but is still quadratic in the number of functions; this is fine for small/medium projects but will need a token-hash scheme for large codebases.

Token savings vs. grep + Read exploration: ~60% fewer tool calls, ~45% fewer tokens on architecture questions spanning multiple files.

---

Quick Start

1. Install

pip install honestcode

Or from source:

git clone https://github.com/Fengrru/honestcode.git
cd honestcode-mcp
pip install -e .

Requires Python >= 3.10

2. Configure your MCP client

Claude Code

claude mcp add honestcode -- honestcode-mcp

Or manually add to ~/.claude.json:

{
  "mcpServers": {
    "honestcode": {
      "command": "honestcode-mcp"
    }
  }
}

Cursor

Add to .cursor/mcp.json (project) or ~/.cursor/mcp.json (global):

{
  "mcpServers": {
    "honestcode": {
      "command": "honestcode-mcp"
    }
  }
}

VS Code

Add to .vscode/mcp.json:

{
  "servers": {
    "honestcode": {
      "command": "honestcode-mcp"
    }
  }
}

Windsurf

Add to ~/.codeium/windsurf/mcp_config.json:

{
  "mcpServers": {
    "honestcode": {
      "command": "honestcode-mcp"
    }
  }
}

Python (direct invocation)

{
  "mcpServers": {
    "honestcode": {
      "command": "python",
      "args": ["-m", "honestcode.mcp.server"]
    }
  }
}

3. Verify setup

Restart your MCP client. The agent should be able to call scan_file. If not, see Troubleshooting.

4. Use it

1. Index your project      →  index_project("/path/to/project")
2. Load dependency APIs    →  load_project_deps("/path/to/project")
3. Verify generated code   →  scan_file("/path/to/project/generated.py")

Typical agent workflow — one call answers the question:

Agent: "Does this code have any hallucinated APIs?"
Tool:  scan_file("src/services/auth.py")
Result: 2 issues found — undefined_call: validate_token (line 12),
                           undefined_call: db.fetch_all (line 27)

---

Environment Variables

Variable	Default	Description
HONESTCODE_TOOLS	scan_file	Comma-separated tool names to expose (or all). scan_file is always included.
HONESTCODE_INDEX_DIR	~/.cache/honestcode	Directory for cached symbol indices
HONESTCODE_CACHE_DIR	~/.cache/honestcode	Directory for SQLite graph caches (override for CI/tests)
HONESTCODE_TIMEOUT	10	Seconds before execute_code is killed
HONESTCODE_MEMORY_MB	256	MB memory limit for sandboxed execution (POSIX)
HONESTCODE_LOG_LEVEL	INFO	Logging verbosity (DEBUG, INFO, WARNING, ERROR)

HONESTCODE_TOOLS

Controls which tools the MCP server exposes. By default only scan_file is registered; set this to a comma-separated list to expose more, or to all to expose every tool:

export HONESTCODE_TOOLS=index,check_symbol,check_api,validate_types
export HONESTCODE_TOOLS=all

scan_file is always included even if not listed. Unknown names are ignored with a warning. Available tool names: scan_file, index, deps, check_symbol, check_api, execute_code, validate_types, find_dead_code, find_similar_code, explore_call_graph, explore_impact, affected_files, stop_watching, search_code, load_package_apis, get_project_stats, choose_tool.

A honestcode.toml config file for per-project rules and ignore patterns is planned — tracked on the Roadmap.

---

Multi-language support (optional)

Python is the fully supported language (stdlib ast). For JavaScript, TypeScript, Go, Rust and Java, symbol extraction is available via the optional tree-sitter extras:

pip install -e "honestcode[multi-language]"

Once installed, scan_file accepts .js/.ts/.go/.rs/.java files and reports undefined call sites using tree-sitter's grammar. Without the extras, scan_file returns a clear message pointing at the install command instead of failing. This keeps the default install dependency-free.

---

Supported Platforms and Agents

Runs anywhere Python 3.10+ does — no native build step, no node_modules, no external services.

Platform	Support
Windows	First-class (stdio + SSE, sandboxed execution)
macOS	First-class (stdio + SSE, sandboxed execution)
Linux	First-class (stdio + SSE, sandboxed execution, RLIMIT limits)

Agent / Client	Config file	Auto-install
Claude Code	~/.claude.json	honestcode install --client claude
Cursor	.cursor/mcp.json	honestcode install --client cursor
VS Code	.vscode/mcp.json	honestcode install --client vscode
Windsurf	~/.codeium/windsurf/mcp_config.json	Manual (see Quick Start)
Any stdio MCP client	command: honestcode-mcp	—
Any SSE MCP client	--transport sse --port 8000	—

See Quick Start for the manual JSON snippets and the CLI Usage section for install/init/root project binding.

---

Tool Reference

Primary tool (always exposed)

scan_file(file_path)

AST-based scan for undefined calls, missing imports, and incorrect API usage in a Python file.

scan_file("/path/to/project/src/auth.py")
# {
#   "success": true,
#   "file": "/path/to/project/src/auth.py",
#   "issues": [
#     {"type": "undefined_call", "name": "validate_token", "line": 12},
#     {"type": "undefined_call", "name": "db.fetch_all", "line": 27}
#   ],
#   "defined_symbols": 342
# }

Issue types: undefined_call — function/method not defined in project or loaded dependencies.

Additional tools (opt-in)

Enable via the HONESTCODE_TOOLS environment variable (see Environment Variables):

export HONESTCODE_TOOLS=index,check_symbol,check_api,execute_code,validate_types

Tool	Purpose	Speed
index_project	Build module-qualified symbol index with content-hash caching	< 1s
load_project_deps	Parse requirements.txt / pyproject.toml and load dependency APIs	< 5s
check_symbol	Verify an identifier is defined in the project	< 5ms
check_api	Verify a library API call exists (with fuzzy typo suggestions)	< 10ms
validate_types	Structural checks: None iteration, wrong arg counts, calling constants	< 20ms
execute_code	Run code in sandboxed subprocess with timeout and memory limits	varies
explore_call_graph	Return callers, callees, and blast-radius summary of a symbol	< 5ms (hot)
explore_impact	Blast radius of a symbol: transitively impacted symbols/files	< 10ms (hot)
affected_files	Files/tests affected by a git diff, via reverse call-graph trace	< 50ms
find_dead_code	Find unused symbols with entrypoint support	< 10ms (hot)
find_similar_code	Detect function-level code clones via sequence similarity	< 2s
search_code	Regex search across project source files (FTS5-accelerated)	< 100ms
load_package_apis	Load API signatures for a single installed package	< 3s
get_project_stats	Return index statistics (symbol count, dependency APIs)	< 5ms
stop_watching	Stop the background file watcher started by index_project(watch=True)	< 5ms
choose_tool	Map a natural-language query to the best tool (debugging)	< 5ms

<details> <summary>Detailed parameter reference</summary>

index_project(root_path, force_rebuild=False, watch=False)

Build or reuse the project symbol index. Returns indexed symbol count, root path, and cache status. Set watch=True to start a background file watcher that re-indexes (and invalidates the graph cache) whenever a source file changes, keeping the index fresh for long-running sessions.

explore_impact(symbol_name, max_depth=3)

Compute the blast radius of a symbol: which other symbols and files would be affected if it changed, following callers and callees up to max_depth hops.

affected_files(base="HEAD", head=None, max_depth=4)

Trace a git diff through the call graph to find which files — especially tests — may be affected by uncommitted changes (base vs the working tree) or a range of commits (base..head). CI-friendly: run it after each commit to know exactly which tests to run.

load_project_deps(root_path)

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

check_symbol(symbol_name, file_path=None)

Verify a symbol is defined in the indexed project. Symbols use module-qualified names (pkg.core.main).

check_api(api_name)

Check if a library API exists. Returns fuzzy suggestions for typos.

check_api("math.sqrt")    # valid
check_api("math.sqrtt")   # invalid → suggests "math.sqrt"

validate_types(code)

Lightweight structural checks on code snippets:

• Iterating over None (including dict.get() without default)
• Wrong argument counts for common builtins (len, sum, etc.)
• Calling constant values
• String methods on non-string constants

execute_code(code, prelude="", known_names=None)

Run code in a sandboxed subprocess with timeout and temp working directory.

explore_call_graph(symbol_name)

Return definitions, callers, and callees of a symbol.

find_dead_code(entrypoints=None, ignore_patterns=None, include_tests=True)

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

find_similar_code(threshold=0.85)

Find function-level code clones across the project. Uses length-ratio pre-filter for performance.

search_code(pattern, glob="*.py")

Regex search across project source files.

load_package_apis(package_name)

Load and cache API signatures for a specific installed package.

get_project_stats()

Return statistics about the currently indexed project.

</details>

---

CLI Usage

Every MCP tool has a CLI equivalent under the honestcode command, for scripts and non-MCP harnesses. Output is JSON; exit code is non-zero when issues are found (so it drops into CI pipelines cleanly).

# Index a project
honestcode index /path/to/project
honestcode index /path/to/project --force

# Load dependency APIs
honestcode deps /path/to/project

# Check a symbol
honestcode check-symbol pkg.core.helper

# Check an API
honestcode check-api pandas.read_csv

# Scan a file (exit 1 if issues found)
honestcode scan src/main.py

# Validate a code snippet (exit 1 if issues found)
honestcode validate "for x in None: pass"

# Execute code in a sandbox
honestcode execute "print(1+1)"

# Find dead code (exit 1 if any dead symbols found)
honestcode dead-code --entrypoints pkg.cli.main --no-tests

# Find similar code (exit 1 if any clones found)
honestcode similar --threshold 0.85

# Explore callers/callees of a symbol (includes blast-radius summary)
honestcode call-graph pkg.core.helper

# Blast radius of a symbol
honestcode impact pkg.core.helper --depth 3

# Files/tests affected by uncommitted changes (CI killer)
honestcode affected --base HEAD
honestcode affected --base main --head feature-branch

# Search code (exit 1 if matches found)
honestcode search "def \w+_helper"

# Load a single package's APIs
honestcode load-package numpy

# Show index statistics
honestcode stats

# Show which tool a query maps to
honestcode choose-tool "is my_symbol defined"

# Bind a directory as a project (creates .honestcode/) and discover the root
honestcode init /path/to/project
honestcode root

# Register the MCP server with Cursor / VS Code / Claude Code
honestcode install --dry-run
honestcode install --client cursor

# Keep an index fresh during long work sessions (Ctrl+C to stop)
honestcode watch /path/to/project

You can also invoke it as a module:

python -m honestcode.cli scan src/main.py

The honestcode-mcp command starts the MCP server (stdio by default); use honestcode-mcp --transport sse --port 8000 for SSE.

---

Library Usage

Every MCP tool is also a plain function in honestcode.mcp.tools, so the same verification logic can run inside your own Python code — no MCP client required:

from honestcode.mcp.tools import check_symbol, index_project, scan_file

index_project("/path/to/project")          # build/reuse the symbol index
print(scan_file("/path/to/project/src/auth.py"))   # hallucination scan
print(check_symbol("pkg.core.main"))               # symbol lookup

Runnable examples live in examples/ — index & check, API typo detection, scan & validate, and dead-code discovery:

pip install -e .
python examples/01_index_and_check.py /path/to/project

---

Architecture

Data flow

graph TD
    Client["MCP Client"] -->|tool call| Tools["tools.py (17 tools)"]
    Tools -->|parse file| Extractor["StructureExtractor (Python ast)"]
    Tools -->|lookup symbol| Index["Symbol Index (cache)"]
    Tools -->|graph queries| Graph["Graph Store (SQLite + FTS5)"]
    Tools -->|check API| KB["Knowledge Base (dep APIs)"]
    Index -->|persists| Graph

Module layout

honestcode/
├── mcp/                    # MCP server layer
│   ├── server.py           # FastMCP entry point (stdio + SSE), tool whitelist
│   ├── tools.py            # 17 tool implementations
│   └── knowledge_base.py   # Dependency API signature cache
├── honest/                 # Core hallucination detection
│   ├── router.py           # NL query → tool routing
│   ├── symbol_index.py     # Project-wide symbol index + caching
│   └── project_binding.py  # .honestcode/ binding + MCP client auto-config
├── graph/                  # Persistent graph layer
│   ├── graph_store.py      # SQLite call graph (definitions/refs) + FTS5 index
│   └── watcher.py          # Zero-dependency polling file watcher
├── structure/              # Code structure extraction
│   ├── extractor.py        # AST-based parser (Python ast)
│   ├── multi_lang.py       # Optional tree-sitter extraction (JS/TS/Go/Rust/Java)
│   ├── relations.py        # Edge/relation data structures
│   └── utils.py            # Shared AST utilities
├── sandbox/                # Sandboxed execution
│   └── __init__.py         # Subprocess executor with timeout + resource limits
└── cli.py                  # Command-line interface (every tool as a subcommand)

Class responsibilities

Module	Class/Function	Responsibility
mcp/server.py	FastMCP	MCP protocol handling, stdio + SSE transport, tool whitelist
mcp/tools.py	Tool functions	17 hallucination-detection tools
mcp/knowledge_base.py	APIKnowledgeBase	Load/cache dependency API signatures via importlib + inspect
honest/symbol_index.py	ProjectIndex	Module-qualified symbol index with content-hash caching
honest/project_binding.py	init/install	.honestcode/ project binding + MCP client auto-configuration
honest/router.py	HonestRouter	Map natural-language queries to tool intents
graph/graph_store.py	GraphCache	SQLite call graph (definitions/refs) + FTS5 full-text index
graph/watcher.py	ProjectWatcher	Polling file watcher with debounce for auto-re-indexing
structure/extractor.py	StructureExtractor	Parse Python AST, extract defs/imports/edges
structure/multi_lang.py	extract_symbols()	Optional tree-sitter extraction (JS/TS/Go/Rust/Java)
structure/utils.py	call_name()	Extract dotted names from AST call nodes
sandbox/__init__.py	SandboxExecutor	Isolated subprocess with timeout + resource limits
cli.py	main()	Argparse-based CLI mirroring every MCP tool

Design decisions

Decision	Rationale
Standard-library ast	Call graphs and file scans use Python's ast module — no native parser dependency, reproducible across platforms
Module-qualified symbols	Index stores pkg.module.func so cross-file references are unambiguous
Persistent graph (SQLite + FTS5)	The call graph is stored on disk keyed by content hashes, so graph queries skip re-parsing; FTS5 narrows regex searches to candidate files
Lazy loading + caching	Dependency APIs and project indices are cached with content-hash invalidation
Zero-dependency watcher	File watching uses stdlib polling + debounce instead of a native watcher, keeping the install footprint small
Thread-safe global state	Tool state protected by RLock for concurrent MCP requests
Subprocess sandbox	execute_code runs in isolation with timeout, memory limits, and restricted PYTHONPATH
Primary tool pattern	One well-aimed tool (scan_file) reduces agent mis-picks vs. 17-tool menu
CLI parity	Every MCP tool has a 1:1 CLI subcommand so the same checks run in CI without an MCP client

Output safety

All tools enforce output limits to prevent context window bloat:

Tool	Max output	Strategy
scan_file	50 issues	Truncated with "truncated": true
check_api	3 suggestions	Fuzzy match capped at top-3
find_dead_code	200 symbols	Filtered by ignore_patterns
find_similar_code	50 pairs	Length-ratio pre-filter
search_code	100 matches	Regex finditer with line limits
explore_call_graph	Full	No limit (bounded by project size)

---

When NOT to use HonestCode

Scenario	Why it doesn't fit	Alternative
Runtime behavior questions	AST is static; can't trace execution	cProfile, py-spy, logging
Non-Python projects	Python is first-class; other languages need [multi-language] extras	CodeGraph (20+ languages)
Type inference across packages	Structural checks only, not full type solver	mypy, pyright
Tiny repos (< 20 files)	Index overhead exceeds benefit	Direct grep
Highly active monorepos	Index may lag behind rapid changes	watch mode or CI-integrated checks

---

Troubleshooting

Symptom	Likely cause	Fix
No tools visible in agent	Server not started	Restart MCP client; check MCP config JSON
Project not indexed error	index_project not called	Call index_project("/path/to/project") first
All symbols report undefined	Dependencies not loaded	Call load_project_deps("/path/to/project")
execute_code timeout	Code contains infinite loop	Increase timeout or fix the code
SyntaxError on scan	File has invalid Python	Fix syntax before scanning
Slow index_project	Large project, first run	Subsequent runs use cache; use force_rebuild=False
Windows: no memory limit	OS limitation	Use Docker/WSL2 for untrusted code

Verify setup

# Check the server is importable
python -c "from honestcode.mcp.server import main; print('OK')"

# Check the CLI works
python -m honestcode.cli --help

# Run tests
python -m pytest tests/ -q

---

Development

# Clone and install
git clone https://github.com/Fengrru/honestcode.git
cd honestcode-mcp
python -m venv .venv
source .venv/bin/activate  # Windows: .venv\Scripts\activate
pip install -e ".[dev]"

# Run tests
pytest

# Lint & format
ruff check honestcode tests scripts
ruff format honestcode tests scripts

# Pre-commit hooks
pre-commit install
pre-commit run --all-files

See CONTRIBUTING.md for pull request guidelines.

---

Security

execute_code runs in a subprocess with:

• Timeout protection (default 10s, configurable)
• Memory limits (256 MB on POSIX via RLIMIT_AS)
• CPU time limits (POSIX via RLIMIT_CPU)
• Restricted PYTHONPATH (empty, no inherited modules)
• Temporary working directory (cleaned up after execution)
• No console window on Windows (CREATE_NO_WINDOW)

This catches accidental mistakes but is not a hardened security boundary. For untrusted code, use a container or dedicated VM.

See SECURITY.md for vulnerability reporting.

---

Telemetry

HonestCode collects no telemetry. There are no analytics libraries, no background services, and no phone-home endpoints:

• All parsing, indexing, and verification run 100% locally — source code never leaves your machine.
• The server makes no outbound network requests of its own. The only network traffic in your stack comes from the LLM provider your MCP client is configured to use.
• Every tool returns deterministic JSON you can diff, so verification results are auditable in CI.

This is a design invariant, not a toggle.

---

Roadmap

• [x] Persistent call graph (SQLite) + FTS5 full-text search
• [x] explore_impact blast-radius analysis
• [x] affected_files git-diff → affected tests (CI killer)
• [x] File watcher for automatic re-indexing
• [x] Project binding (.honestcode/) + install for MCP clients
• [x] Multi-language symbol extraction via optional tree-sitter extras
• [ ] VS Code extension with inline diagnostics
• [ ] GitHub Action for PR-level hallucination checks
• [ ] Remote dependency API caching (PyPI index)
• [ ] Configurable rules and ignore patterns
• [ ] Adaptive output budgeting based on project size

---

Changelog

See CHANGELOG.md for release history.

---

Contributing

Contributions are welcome! Please read CONTRIBUTING.md first.

---

License

MIT - Copyright (c) 2026 HonestCode Team