codesynapse-cli 0.1.2

Code intelligence MCP server — gives AI coding assistants architecture-level knowledge of your codebase.

Quick Start · MCP Tools · Languages · Configuration · Uninstall · Troubleshooting · Contributing

---

AI coding tools answer questions about individual files well. They cannot reason about architecture — class hierarchies, call chains, blast radius of a change, which module owns a concept. grep and file search return noise, not signal.

Codesynapse fixes this. It builds a structural knowledge graph from your source code (nodes = classes, functions, files; edges = calls, extends, implements, contains), merges graphs from multiple modules into a single global graph, and exposes 32 MCP tools backed by hybrid BM25 + dense vector search. Every session with Claude Code or Cursor starts with full graph context — not a blank slate.

Runs entirely local. No GPU, no cloud APIs, no infrastructure.

---

Demo

---

Why codesynapse?

	Python graphify	graphify-rs	semble	code-review-graph	codegraph	Sourcegraph Cody	continue.dev	codesynapse
Language	Python	Rust	Python	Python	TypeScript	Cloud	VS Code ext.	Rust
MCP tools	✗	✗	2	30	10	✗	✗	32
Structural graph	Partial	General KG	✗	✓	✓	✓	✗	✓
Blast radius	✗	✗	✗	✓	✓	✓	✗	✓
Hybrid BM25 + dense	✗	BM25 only	✓	Optional	✗ (FTS5)	✓	✗	✓
Fully local	✓	✓	✓	✓	✓	✗	✗	✓
No cloud API needed	✓	✓	✓	✗ (semantic)	✓	✗	✗	✓
Multi-module graph	✗	✗	✗	✓	✓	✓	✗	✓
Cross-module hierarchy	✗	✗	✗	✗	✓	✓	✗	✓
File reads eliminated	—	—	—	—	100%	—	—	100%
No telemetry by default	✓	✓	✓	✓	✗ (opt-out)	✗	✗	✓ (opt-in)
Runtime	Python	Rust	Python	Python	Node.js	Cloud	Node.js	Rust binary

codegraph is the closest alternative — TypeScript, local, 10 MCP tools, blast radius, multi-module. Key gap: lexical FTS5 search only (no dense embeddings), so synonym and concept queries miss results that BM25+dense RRF catches. semble uses the same Model2Vec + BM25 + RRF search stack but is search-only — no structural graph, no blast radius, no hierarchy. code-review-graph has graph + MCP but is Python and requires a cloud API for semantic search. graphify-rs is the Rust rewrite of the original Python graphify tool — general-purpose knowledge graphs, not MCP-native or code-intelligence-focused.

Codesynapse is the Rust rewrite of Python graphify with full MCP integration, structural graph analysis, and zero cloud dependencies.

---

How it works

flowchart TD
    A[("Source code\n(any repo)")] -->|parallel tree-sitter AST\n30+ languages| B["per-module graph.json"]
    B -->|global_add — prefix node IDs, merge| C[("global-graph.json\n~/.codesynapse/")]
    C -->|embed_global_graph\npotion-code-16M · CPU-only · mtime-gated| D[("embeddings.json\n~/.codesynapse/")]
    C & D --> E[["MCP server\n32 tools · hybrid BM25 + dense RRF"]]
    E --> F["Claude Code · Cursor · OpenCode\nCodex CLI · Hermes · Kiro · any MCP client"]

    style A fill:#f6f8fa,stroke:#57606a,color:#24292f
    style B fill:#ddf4ff,stroke:#54aeff,color:#0550ae
    style C fill:#dafbe1,stroke:#4ac26b,color:#1a7f37
    style D fill:#fff8c5,stroke:#d4a72c,color:#4d2d00
    style E fill:#ede9fe,stroke:#8957e5,color:#512a97
    style F fill:#ffeef8,stroke:#bf3989,color:#6e1e5c

Key design choices:

Decision	Reason
Hybrid BM25 + dense RRF	BM25 handles symbol names precisely; dense closes the synonym gap. RRF fusion gives best of both.
Model2Vec potion-code-16M	Static embeddings — no forward pass at query time, ~1.5ms queries, CPU-only, 64 MB model.
Sled embedded DB	Zero-dependency, file-based, fast random access by node ID. No server process.
Tree-sitter AST extraction	Grammar coverage across 30+ languages. No language server or build system required.
Per-module → global merge	Enables cross-module blast radius and hierarchy without loading all modules into memory.
Mtime-gated embedding regen	Embeddings only regenerated when global-graph.json is newer. Zero overhead for unchanged graphs.

---

Language support

Group	Languages
Systems	Rust, C, C++, Go, Zig, Fortran, Verilog
JVM	Java, Kotlin, Scala, Groovy
Web / Frontend	JavaScript, TypeScript, Svelte, Vue, PHP
Scripting	Python, Ruby, Lua, Bash, PowerShell
Mobile / Apple	Swift, Objective-C, Dart
Functional	Haskell, Elixir, Racket, Julia
Other	SQL, C#, CMake, Pascal

---

Installation

Prerequisites:

• ~500 MB free disk (graph store + model, downloaded on first setup)
• Internet connection on first run (model download only)

Option A — One-liner

Linux / macOS:

curl -fsSL https://raw.githubusercontent.com/sohilladhani/codesynapse/master/install.sh | sh

Windows (PowerShell):

irm https://raw.githubusercontent.com/sohilladhani/codesynapse/master/install.ps1 | iex

Or download a specific binary from releases:

Platform	Binary
Linux x86_64	codesynapse-linux-x86_64
macOS Apple Silicon	codesynapse-macos-aarch64
Windows x86_64	codesynapse-windows-x86_64.exe

chmod +x codesynapse-*
sudo mv codesynapse-* /usr/local/bin/codesynapse

Option B — Package managers

macOS (Homebrew):

brew tap sohilladhani/codesynapse
brew install codesynapse

Windows (Scoop):

scoop bucket add cs https://github.com/sohilladhani/scoop-codesynapse
scoop install codesynapse

Nix:

nix run github:sohilladhani/codesynapse        # run directly
nix profile install github:sohilladhani/codesynapse  # install permanently

Or add to your flake:

inputs.codesynapse.url = "github:sohilladhani/codesynapse";
# then: inputs.codesynapse.packages.${system}.default

Option C — Build from source

Requires Rust stable toolchain (install):

cargo install codesynapse-cli

---

Quick start

# 1. Register the MCP server with Claude Code and/or Cursor (auto-detects both)
codesynapse setup

# Other clients (if not auto-detected):
codesynapse opencode install  # OpenCode
codesynapse codex install     # Codex CLI
codesynapse hermes install    # Hermes Agent
codesynapse kiro install      # Kiro

# 2. Index a repository
codesynapse module add myrepo /path/to/your/repo

# 3. Restart your AI client

# 4. Ask architecture questions — the 32 MCP tools are now available

That's it. From this point, queries like "what handles auth token expiry?" or "show blast radius of UserService" are answered from the graph — not from file search.

Add more repositories:

codesynapse module add backend /path/to/backend
codesynapse module add frontend /path/to/frontend
# Graphs are merged — cross-module queries work automatically

Refresh after code changes:

codesynapse module refresh myrepo

List indexed modules:

codesynapse module list

Remove a module:

codesynapse module remove myrepo
# Prunes its nodes from the global graph and deregisters it

Keep the graph current with git (optional):

codesynapse hook install   # installs a post-merge git hook — auto-refreshes on pull

---

MCP tools

32 tools across six categories, callable from Claude Code, Cursor, or any MCP-compatible client.

Category	Tools
Graph search	codesynapse_query_vector, codesynapse_query_semantic, codesynapse_blast_radius, codesynapse_blast_radius_scored, codesynapse_blast_radius_multi, codesynapse_hierarchy, codesynapse_list_graphs, codesynapse_module_summary, codesynapse_build
Code reading	codesynapse_resolve, codesynapse_outline, codesynapse_read, codesynapse_read_method, codesynapse_read_with_callees
Navigation	codesynapse_find_callers, codesynapse_find_usages
Graph analysis	codesynapse_query_graph, codesynapse_get_node, codesynapse_get_neighbors, codesynapse_get_community, codesynapse_god_nodes, codesynapse_graph_stats, codesynapse_shortest_path, codesynapse_find_all_paths, codesynapse_weighted_path, codesynapse_community_bridges, codesynapse_diff, codesynapse_pagerank, codesynapse_detect_cycles, codesynapse_smart_summary, codesynapse_find_similar
Observability	codesynapse_stats

Full parameter reference and examples: docs/MCP-TOOLS.md

Common queries in Claude Code:

"What handles auth token expiry?"          → codesynapse_query_vector
"Show blast radius of UserService"         → codesynapse_blast_radius
"What does UserRepository extend?"         → codesynapse_hierarchy
"Read the validate() method"               → codesynapse_read_method
"Who calls PaymentService.charge()?"       → codesynapse_find_callers

---

Configuration

Place codesynapse.toml in your project root. All fields are optional.

# Output directory for exported graph (default: codesynapse-out/)
output = "codesynapse-out"

# Skip LLM extraction for doc/paper files (default: false)
no_llm = false

# Index source code only, skip docs and papers (default: false)
code_only = false

# Export formats: "json", "html", "graphml", "obsidian"
formats = ["json", "html"]

# LLM config for semantic extraction of docs/papers (optional)
[llm]
provider = "anthropic"           # "anthropic" | "openai" | any OpenAI-compatible
model = "claude-sonnet-4-20250514"
api_key = "sk-..."               # or set ANTHROPIC_API_KEY / OPENAI_API_KEY env var
base_url = "https://..."         # optional, for OpenAI-compatible providers

# Custom model path (default: auto-resolved by codesynapse setup)
[embeddings]
model_path = "./models/potion-code-16M"

---

Repository layout

codesynapse/
├── codesynapse-core/       # Extraction, graph, embedding, global graph
├── codesynapse-cli/        # CLI binary (module add/refresh/list, build, setup)
├── codesynapse-mcp/        # MCP server — 32 tools, JSON-RPC over stdio
├── codesynapse-serve/      # BM25 + dense hybrid search engine
├── codesynapse-tui/        # Terminal UI
├── codesynapse-grpc/       # gRPC server
├── codesynapse-graphql/    # GraphQL API
├── codesynapse-wasm/       # WebAssembly bindings
├── models/
│   └── potion-code-16M/    # Static embedding model (downloaded by setup)
├── tests/                  # Integration tests
└── docs/
    ├── ARCHITECTURE.md
    └── MCP-TOOLS.md

Runtime data lives in ~/.codesynapse/:

~/.codesynapse/
├── global-graph.json       # Merged graph (all modules)
├── embeddings.json         # node_id → Vec<f32> dense embeddings
├── modules.conf            # name|/path module registry
├── global-manifest.json    # Per-module hash + metadata
├── tool_stats.jsonl        # MCP tool call log
├── models/potion-code-16M/
└── modules/<name>/graph.json

---

Uninstall

Remove from all AI clients:

# Re-run setup and remove the entry manually from the config files setup wrote:
#   Claude Code:  ~/.claude.json       (key: mcpServers.codesynapse)
#   Cursor:       ~/.cursor/mcp.json   (key: mcpServers.codesynapse)
#   Windsurf:     ~/.codeium/windsurf/mcp_config.json
#   OpenCode:     ~/.config/opencode/opencode.json

Remove a specific module:

codesynapse module remove myrepo

Full cleanup (removes all indexed data):

rm -rf ~/.codesynapse/

---

Manual MCP setup

If codesynapse setup doesn't auto-detect your client, add this entry manually:

Claude Code (~/.claude.json):

{
  "mcpServers": {
    "codesynapse": {
      "type": "stdio",
      "command": "codesynapse",
      "args": ["mcp"]
    }
  }
}

Cursor (~/.cursor/mcp.json):

{
  "mcpServers": {
    "codesynapse": {
      "type": "stdio",
      "command": "codesynapse",
      "args": ["mcp"]
    }
  }
}

For other clients, pass the same command/args pair to their MCP server config.

---

CLI skill (MCP-free fallback)

If MCP is blocked by your org's network policy, codesynapse ships a CLI skill for Claude Code and a rules file for Cursor. Your AI client shells out to codesynapse directly instead of using the MCP protocol.

Claude Code — copy into your project:

mkdir -p /path/to/your/project/.claude/skills
cp -r integrations/claude-code/skills/codesynapse-cli /path/to/your/project/.claude/skills/

Cursor — copy into your project:

mkdir -p /path/to/your/project/.cursor/rules
cp integrations/cursor/rules/codesynapse-cli.mdc /path/to/your/project/.cursor/rules/

The integrations/ directory ships with the repository. Restart your client after copying.

---

pi extension

For pi users, install the codesynapse extension:

pi install npm:codesynapse-pi

This wires up 12 curated codesynapse tools and injects graph-awareness into every pi session automatically.

---

Troubleshooting

MCP server not connecting

• Verify codesynapse is on your PATH: which codesynapse
• Run codesynapse setup again — it re-writes the client config
• Restart your AI client after setup

No results from graph queries

• Check modules are indexed: codesynapse module list
• Rebuild the global graph: codesynapse build
• Ensure the model downloaded: codesynapse setup (downloads potion-code-16M on first run)

Stale results after code changes

• Refresh the module: codesynapse module refresh myrepo
• Or install the git hook for automatic refresh: codesynapse hook install

codesynapse setup says no embedding model

codesynapse setup downloads the model automatically. If it fails:

1. Check your internet connection and re-run codesynapse setup
2. Download manually from HuggingFace:

   https://huggingface.co/minishlab/potion-code-16M/resolve/main/model.safetensors
   https://huggingface.co/minishlab/potion-code-16M/resolve/main/tokenizer.json
   https://huggingface.co/minishlab/potion-code-16M/resolve/main/config.json
   

   Place all three files in ~/.codesynapse/models/potion-code-16M/, then re-run codesynapse setup.

Graph query is slow

• First query after startup is slower — embeddings load from disk
• Subsequent queries are fast (~1.5 ms encode + BM25 + cosine)

---

Telemetry

Telemetry is off by default. Enable it explicitly if you want to help improve codesynapse:

codesynapse telemetry on    # opt in
codesynapse telemetry off   # opt out + delete local queue

When enabled, codesynapse sends anonymous daily rollups: tool names, call counts, and coarse token-savings buckets. No query content, no file paths, no source code, no IPs. See TELEMETRY.md for the full data contract.

---

Contributing

Contributions welcome. Please read CONTRIBUTING.md before opening a PR.

• Bug reports: use the bug report template
• Feature requests: use the feature request template
• Code: run cargo test --workspace and cargo clippy --workspace -- -D warnings before submitting

This project follows the Contributor Covenant code of conduct.

---

License

MIT — see LICENSE.