🌳 Tree-sitter Analyzer

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Code intelligence AI agents can trust — correct cross-language structure across 20+ languages, agent-native (MCP + CLI).

TSA indexes your codebase with tree-sitter and serves correct call graphs, symbol search, and structural queries to AI coding agents — locally, with no telemetry.

Why it's different:

• Cross-language correctness is the moat. A name-only index wires Python sorted() to a Swift func sorted. TSA doesn't. ~390× fewer cross-language call-graph mis-wires than alternatives (reproducible audit).
• Built agent-native. 8 MCP tools, TOON output (~half the size of JSON on bulk/tabular responses), verdict envelopes, and 13 curated Skills — designed for Claude Code, Cursor, and any MCP client.
• Broad and correctly classified. 13 languages with full call-graph indexing (Python · Go · Rust · Java · JS · TS · C · C++ · C# · Swift · Kotlin · Ruby · PHP), 8 more symbol-indexed or CLI-reachable.

Proof: on HuggingFace tokenizers (Rust+Python+JS+TS), a name-only resolver mis-wires 1,259 call edges — TSA: 0. Run it on your repo in seconds: uvx --from tree-sitter-analyzer miswire-audit .

Upgrading from v1.x? See docs/MIGRATION.md.

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Get Started

Requires Python 3.10+ (check: python3 --version). Install from python.org if needed.

One-line install for Claude Code:

claude mcp add tree-sitter-analyzer \
  --env TREE_SITTER_PROJECT_ROOT="$PWD" \
  -- uvx --from "tree-sitter-analyzer[mcp]" tree-sitter-analyzer-mcp

Restart your agent, then say: "Run the index tool with action=status." CLI equivalent (no agent needed): tree-sitter-analyzer --codegraph-status

PyPI / uvx users — install skills: the 13 tsa-* skills are bundled in the wheel. Copy them once with:

tree-sitter-analyzer --install-skills              # into ./.claude/skills/ (this project)
tree-sitter-analyzer --install-skills-global       # into ~/.claude/skills/ (all projects)

Git-clone users already have them under .claude/skills/ — no action needed.

Other agents (Cursor, Copilot, Cline, Continue, Claude Desktop, Roo Code) →

Quick install

1. Install dependencies

# uv (required)
curl -LsSf https://astral.sh/uv/install.sh | sh        # macOS / Linux
powershell -ExecutionPolicy ByPass -c "irm https://astral.sh/uv/install.ps1 | iex"  # Windows

# fd + ripgrep (required for `search action=content` text search; symbol search uses SQLite FTS5 and needs neither)
brew install fd ripgrep                                # macOS
winget install sharkdp.fd BurntSushi.ripgrep.MSVC      # Windows

2. Install Tree-sitter Analyzer

# Standalone install (persistent CLI command):
uv tool install "tree-sitter-analyzer[all,mcp]"
# — or skip installing entirely: the MCP entry below runs via uvx on demand.
# Inside a uv-managed Python project, use: uv add "tree-sitter-analyzer[all,mcp]"

3. Hook it into your agent

See Supported Agents. Most clients want this MCP server entry:

{
  "mcpServers": {
    "tree-sitter-analyzer": {
      "command": "uvx",
      "args": ["--from", "tree-sitter-analyzer[mcp]", "tree-sitter-analyzer-mcp"],
      "env": { "TREE_SITTER_PROJECT_ROOT": "/absolute/path/to/your/project" }
    }
  }
}

After restart: "Run the index tool with action=status." CLI equivalent (no agent needed): tree-sitter-analyzer --codegraph-status

See the correctness edge on your own repo — no install, no CodeGraph (it re-indexes first; seconds on a small repo, a minute or two on a large one):

uvx --from tree-sitter-analyzer miswire-audit .

It prints how many call edges a name-only code index (the design most tools use) would mis-wire across a language boundary — e.g. a Python sorted() wired to a Swift func sorted — versus how many TSA does (≈0). On HuggingFace tokenizers: 1,259 → 0.

---

Why Tree-sitter Analyzer

• Token-efficient on bulk output. Every MCP response uses TOON, a tabular JSON variant that cuts bulk/tabular payloads by roughly half vs raw JSON (measured invariant). Note: small metadata-heavy decision-tool responses are currently ~equal-to-larger than JSON under the present envelope wiring — tracked by a strict-xfail invariant and being corrected in RFC-0018.
• Verdict envelopes. Every response carries verdict: SAFE | CAUTION | UNSAFE | INFO | REVIEW | WARN | ERROR | NOT_FOUND, so orchestrators branch on outcomes without re-prompting.
• Project health grading (A–F). Few code-intel tools expose a whole-project quality grade — TSA grades on size / complexity / coverage / duplication / dependencies / structure / git-hotspots in one call.
• 13 curated workflows (Skills). Pre-baked tool subsets for "find symbol", "trace call chain", "score health", "safe-to-edit before refactor", "PR review", etc.
• 5 layers of safety. edit action=safe + edit action=guard + constraint DSL + edit action=impact + verdict envelopes — designed so agents know before they touch.
• Strict CLI superset of CodeGraph, faster indexing, and a one-call query DSL — with an honest cost comparison (below).

---

Key Features

Pre-indexed code intelligence (CodeGraph parity + superset)

Capability	TSA tool	Status
Symbol search (FTS5 + BM25 ranked)	search action=symbol	ahead — results sorted by relevance score, not file path
Go-to-def / find-refs / call hierarchy in one call	nav action=navigate	PRIMARY entry point
Bulk-fetch N related symbols + relationship map	structure action=explore	parity
Function-level blast radius + risk score	nav action=impact	parity + risk score
Who-calls-X / what-X-calls	nav action=callers / action=callees	parity
Index health at-a-glance (+ edge count)	index action=status	ahead — reports total_edges for graph density signal
Pre-built call graph cache	index action=auto / action=full / action=sync	parity
Tests affected by a change (CLI)	--affected FILE...	parity

Tree-sitter Analyzer exclusive

Capability	TSA tool	Note
BM25-ranked symbol search	all search tools	relevance_score on every result (min-max normalized: best=1.0, weakest=0.0); sort(by='confidence') in DSL
Semantic search (BM25 pre-filtered)	search action=chain (semantic() DSL)	BM25 pre-filter narrows 40k symbols to ~400 before cosine rerank
Project A–F health grading	health action=project	7 dimensions (size/complexity/deps/coverage/duplication/structure/git-hotspot), uncommon among code-intel tools
TOON output	every tool, output_format: "toon" (default)	~50 % token saving on bulk/tabular output (decision tools tracked by RFC-0018)
Verdict envelopes	every tool	SAFE/CAUTION/UNSAFE/INFO/WARN/ERROR/NOT_FOUND
Safe-to-edit gate	edit action=safe / action=guard	refuses high-risk edits before they happen
Architectural constraint DSL	edit action=constraints	"module A cannot import B" → enforced
Code health (file-level)	health action=file	block/long-method/smell detection
Class hierarchy	structure action=class_tree	type-inheritance tree
Dependency matrix	health action=matrix	module-coupling matrix
Dead code	health action=dead	transitive unreachable analysis
Complexity heatmap	health action=heatmap	per-fn cyclomatic + project view
AST-structural clone detection	viz action=similarity	beyond text similarity
Mermaid call-graph export	viz action=graph	paste-ready in docs
UML Mermaid export	viz action=uml	class / package / component / sequence diagrams
PR review	edit action=pr	AST-diff + semantic classify + blast radius
agent_summary	every response	next-step hint baked into the envelope
Synapse cross-file resolver	internal	import-aware, beats regex guessing
Temporal activation	nav action=lineage	per-symbol git-modification frequency
One-shot file orientation	project action=smart	health + exports + deps + edit-risk in one call (replaces 3-4 calls)
Architectural decision journal	project action=journal	persists reasoning across sessions — uncommon among code-intel tools

Skills (13 curated workflows)

CodeGraph has zero skills. We ship 13 under .claude/skills/tsa-*/:

tsa-landing, tsa-find, tsa-graph, tsa-structure, tsa-deps, tsa-index, tsa-health-watch, tsa-edit-safety, tsa-edit-then-verify, tsa-constraints, tsa-pr-review, tsa-refactor-queue, tsa-temporal.

Each skill ships an allowed-tools subset + procedure recipe + decision-surface schema, so the agent doesn't have to triage 8 tools on every question.

312 CLI flags

Superset of CodeGraph's CLI surface. Highlights:

tree-sitter-analyzer --table full <file>          # method/signature/complexity table
tree-sitter-analyzer --partial-read --start-line N --end-line M <file>
tree-sitter-analyzer --project-health             # A-F grade across the project
# Note: --callers / --callees require the call-graph index — run --full-index first
tree-sitter-analyzer --full-index                 # build call-graph index (run once)
tree-sitter-analyzer --callers <symbol>           # who-calls
tree-sitter-analyzer --codegraph-impact <fn>      # blast radius + risk
tree-sitter-analyzer --affected <file...>         # tests transitively affected
tree-sitter-analyzer --dead-code                  # transitive unreachable
tree-sitter-analyzer --check-constraints          # architectural rules
tree-sitter-analyzer --safe-to-edit <file>        # refuse if risky
tree-sitter-analyzer --uml class                  # Mermaid UML class diagram

Installing the package also registers three standalone search utilities (thin entry points over the same engine, handy in shell pipelines):

list-files <dir>          # fd-style file discovery
search-content <pattern>  # ripgrep-style content search
find-and-grep <pattern>   # two-stage fd + ripgrep

See docs/CODEMAPS/cli.md for the full surface.

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How TSA compares to CodeGraph

Call-graph correctness — TSA resolves what CodeGraph mis-wires

Token cost is one axis; a code-intelligence tool's first job is a correct graph.

Head-to-head on this repo, both tools' live indexes (count every call edge whose caller language differs from the callee's — a cross-language mis-wire by construction; reproducible):

tool	cross-language mis-wires	total call edges	rate
CodeGraph	745	38,103	1.96 %
Tree-sitter Analyzer	6	114,160	0.005 %

~390× cleaner on cross-language correctness, while resolving 3× more call edges. CodeGraph's mis-wires span 19+ language pairs (python→swift 408, python→typescript 195, python→ruby 81, …); TSA's 6 are all java→python/php from single-word Java method names.

Don't trust this table — run it on your own repo (no CodeGraph install needed):

uvx --from tree-sitter-analyzer miswire-audit .

It indexes your code and prints how many call edges a name-only resolver (the design most indexes use) would mis-wire across a language boundary vs how many TSA does — with the offending edges listed (Python sorted() → Swift func at file:line). Add --card for a shareable scorecard.

Real runs: on HuggingFace tokenizers (Rust+Python+JS+TS) a name-only resolver would mis-wire 1,259 call edges (incl. a JS tokenize() → Rust def) — TSA: 0. On a single-language repo (gin, Go) both are 0 — no false positives. More examples →

Concretely:

call (Python _resolve_entry_points / build_response)	CodeGraph	TSA
sorted() (Python builtin)	❌ callee = tests/golden/corpus_swift.swift — a Swift func sorted (wired as a callee of 299 Python functions repo-wide)	✅ builtin — no cross-language edge
fts_search() / fts_search_ranked()	❌ bound to the test mock (FallbackCache) instead of the real method	✅ resolves to the source method (_ast_cache_query.py / ast_cache.py)

TSA's per-language resolver gates every binding by language family across 13 languages (Python · Java · Go · JS · TS · C · C++ · Rust · C# · Kotlin · Ruby · PHP · Swift) and demotes test-only definitions for non-test callers, across all of its resolution paths. Telling an agent that a Python function calls a Swift method, or that a production call targets a test mock, is wrong structural data — and it is the dominant failure mode of a name-only index.

Correct and complete — 96.3% of call edges classified

A correct graph that leaves most edges unknown is still half a graph. TSA's resolution cascade now classifies 96.3% of call edges (up from 83.9%), with zero cross-language or test-shadow mis-wires — every gain is gated on the project owning no compatible-language symbol of that name, so shadowing is always preserved:

resolver tier	what it resolves	source
binding cascade	local / self / import / unique-method / single-global	RFC-0002
stdlib method names (write_text, strip, items)	str / Path / dict / re / argparse methods → stdlib	RFC-0004
external library methods (raises, given, MagicMock)	pytest / hypothesis / mock → external	RFC-0005

The remaining ~4% unknown is dominated by genuinely-unresolvable dynamic dispatch (BaseTool.execute()), constructors, and ambiguous same-name project methods — the false-positive floor of static analysis, left honest rather than guessed.

Now multi-language. Cross-language-safe resolution is no longer Python-only. A per-language resolver registry (RFC-0010) gives each language its own classification cascade with conservative stdlib/external tiers, gated by language family so a binding does not cross into an incompatible language. Active classified call graph (call-edge extraction + per-language resolver), 13 languages: Python · Java · Go · JavaScript · TypeScript · C · C++ · Rust · C# · Kotlin · Ruby · PHP · Swift. Each has its own conservative stdlib/external tiers and is adversarially verified to never bind across a language boundary. Swift is notable: CodeGraph's flagship mis-wire binds 299 Python sorted() callers to a Swift func sorted — TSA resolves Swift correctly and refuses that exact cross-language bind (verified both directions). Measured on the active set: 6 cross-language edges (6 of ~57,000 resolved edges, all generic 1-word Java method names) — ~390× cleaner than CodeGraph on cross-language correctness, which wires 299 Python sorted() callers to a single Swift func sorted (TSA binds 0 of 298). Full reproducible audit: benchmarks/codegraph_compare/REPORT-v1.21.0.md. Adding a language is one new resolver file (RFC-0010) plus a small call-extraction wiring.

Symbol kinds, too. TSA classifies class members as kind=method (20,348 method rows on this repo) — search action=symbol kind=method returns them; CodeGraph parity, not a stub. The index status payload breaks symbols down by kind and language and edges by kind (edges_by_kind — a breakdown CodeGraph does not surface).

Where TSA leads

• Index build speed. Removing a redundant post-index edge-refresh pass cut a cold django index (~2 950 files) from 181 s → 97 s (−46 %); the win grows with repo size. Re-index of unchanged files is a content-hash lookup.
• Strict CLI superset. Every MCP tool has a CLI equivalent (CodeGraph's CLI is thinner); behavioural defaults (ranking, limits, truncation) are kept in lock-step between the two surfaces. Output format is the one intentional divergence — MCP defaults to TOON (token-efficient for agents), the CLI to JSON (human/jq-friendly).
• One-call expressiveness. A jQuery-style chain DSL — search('X').callees(depth=2).explore(include_code=true).answer(compact=true) — returns an entire flow's subgraph + source in a single call, with JS-style true/false so agents can write it naturally.
• Output is structured + token-aware. TOON default for MCP (~half the size of JSON on bulk/tabular output; decision-tool wiring corrected in RFC-0018), per-call truncation hints, consistent test-file de-prioritisation across every ranking path.
• Breadth. Health scoring, safe-to-edit / change-impact gating, 13 curated Skills, and broad language coverage.

On token cost — and a benchmark we corrected

Correction (2026-06). An earlier version of this section claimed TSA beat CodeGraph on agent token cost (a "−11 % median" table). That benchmark had a harness bug: the TSA arm's MCP server was started without an explicit project root and analysed tree-sitter-analyzer's own source instead of the target repo, so its numbers were meaningless. The bug is fixed (the harness now passes --project-root), the inflated claim is withdrawn, and the honest picture is below.

Token cost was the one axis where CodeGraph led. RFC-0006 progressive disclosure closes most of the gap at the source: nav context now returns a lean default — entry points + a compact related_symbols list + code blocks — and moves the flat node/edge graph behind an opt-in include_graph=true. Measured on this repo (4 representative queries, TOON):

context payload	chars
TSA default, before RFC-0006	~13,900
TSA default, after (lean)	~6,600 (−53%)
TSA include_graph=true (full, opt-in)	~13,900
CodeGraph baseline	~4,400

The dominant context call went from ~2.9× CodeGraph's payload to ~1.5×.

For context, the per-task $ cost measured before RFC-0006 (corrected harness — Claude Sonnet, gin + django, MCP arms, no errors):

arm	median cost (pre-RFC-0006)	tool calls	file reads
CodeGraph MCP	~$0.27	7	2
Tree-sitter Analyzer MCP	~$0.44	7	1
no-MCP (grep/read)	~$0.34	14	7

A full per-task $ re-benchmark is the next measurement (harness command below). We report the payload proxy straight rather than restate the old table as if RFC-0006 hadn't shipped.

Reactive push + edge-kind breakdown — two things CodeGraph can't do

CodeGraph (and most one-shot indexers) only answer on poll: you ask, it replies with a snapshot, and you re-ask to learn whether anything changed. TSA exposes two capabilities that close that loop:

• Reactive push / subscription (RFC-0001, implemented). search action=subscribe registers a Hyphae selector and returns a tsa://hyphae/{selector} MCP resource URI. When the watched code changes, the server emits a resource-updated notification — the agent re-reads the resource instead of polling. search action=unsubscribe cancels it. CodeGraph has no push or subscription channel.
• edges_by_kind in index action=status. Status returns a per-edge-kind count (calls / extends / implements / imports …), not just a single total_edges — so an agent can read the graph's shape (how call-heavy vs inheritance-heavy a repo is) before drilling in. CodeGraph surfaces only a flat total.

Reproduce the correctness fixes on any repo both tools have indexed:

# CodeGraph: emits the cross-language / test-shadow callee
#   (e.g. `sorted` → corpus_swift.swift, `fts_search` → test mock)
# TSA after the resolver fix: language-correct, source-preferring
tree-sitter-analyzer --callees _resolve_entry_points --format json

Reproduce the cost numbers: uv run python benchmarks/codegraph_compare/run.py phase full-warm --repos gin,django. Raw envelopes + the harness fix live in that directory.

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How It Works

Source code → tree-sitter parse → SQLite + FTS5 index (.ast-cache/index.db)
                                         ↓
        nav (navigate) / structure (explore) / nav (callers) / ...
                                         ↓
                            TOON-encoded envelope
                            (compact for tabular output;
                             verdict + agent_summary + data)
                                         ↓
                              MCP client / CLI consumer

The index is built lazily on first query, refreshed on file change via a content-hash diff (index action=sync). All 8 tools read from the same .ast-cache/, so a query and its follow-up share work.

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Supported Agents

📘 Claude Code (recommended)

claude mcp add tree-sitter-analyzer \
  --env TREE_SITTER_PROJECT_ROOT="$PWD" \
  -- uvx --from "tree-sitter-analyzer[mcp]" tree-sitter-analyzer-mcp

Verify: claude mcp list. The 13 tsa-* skills auto-discover from .claude/skills/.

PyPI / uvx users — install the bundled skills once with:

tree-sitter-analyzer --install-skills              # into ./.claude/skills/ (this project)
tree-sitter-analyzer --install-skills-global       # into ~/.claude/skills/ (all projects)

Git-clone users already have them — no action needed.

📗 Claude Desktop

Edit claude_desktop_config.json (macOS: ~/Library/Application Support/Claude/, Windows: %APPDATA%\Claude\, Linux: ~/.config/Claude/):

{
  "mcpServers": {
    "tree-sitter-analyzer": {
      "command": "uvx",
      "args": ["--from", "tree-sitter-analyzer[mcp]", "tree-sitter-analyzer-mcp"],
      "env": { "TREE_SITTER_PROJECT_ROOT": "/absolute/path/to/your/project" }
    }
  }
}

📙 GitHub Copilot (VS Code)

Create .vscode/mcp.json (note: servers, not mcpServers):

{
  "servers": {
    "tree-sitter-analyzer": {
      "type": "stdio",
      "command": "uvx",
      "args": ["--from", "tree-sitter-analyzer[mcp]", "tree-sitter-analyzer-mcp"],
      "env": { "TREE_SITTER_PROJECT_ROOT": "${workspaceFolder}" }
    }
  }
}

🖱 Cursor / Cline / Continue / Roo Code

All read the same mcpServers schema as Claude Desktop. Cursor: Settings → MCP. Cline: MCP panel → Edit settings. Continue: ~/.continue/config.json under experimental.modelContextProtocolServers. Roo Code: MCP panel → Edit MCP Settings.

🐳 Docker (no local Python / uv)

The repo ships a Dockerfile that builds the MCP server (stdio transport) from source, so the image always matches the committed code.

# Build once
docker build -t tree-sitter-analyzer-mcp .

# Run against the current repo (server speaks MCP over stdio; -i keeps stdin open)
docker run --rm -i --user "$(id -u):$(id -g)" \
  -v "$PWD:/work" -w /work tree-sitter-analyzer-mcp

--user "$(id -u):$(id -g)" runs as your host UID/GID, so the .ast-cache/, decision journal, and any edit writes under the bind-mounted repo are owned by you, not root.

MCP client config (the project root inside the container is the mount point /work):

{
  "mcpServers": {
    "tree-sitter-analyzer": {
      "command": "docker",
      "args": [
        "run", "--rm", "-i",
        "--user", "1000:1000",
        "-v", "/absolute/path/to/your/project:/work",
        "-w", "/work",
        "-e", "TREE_SITTER_PROJECT_ROOT=/work",
        "tree-sitter-analyzer-mcp"
      ]
    }
  }
}

⚠️ TREE_SITTER_PROJECT_ROOT must be absolute. The server enforces a security boundary against escapes via SecurityValidator.

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Supported Languages

21 language plugins; 13 fully wired into the indexer (full symbol + call graph) + 2 symbol-indexed (call-graph wiring pending) + 5 (data/markup) reachable via the single-file CLI path + 1 scaffold (plugin exists, indexer wiring pending). bash and scala graduated in v1.22.0; the 2026-05-24 patch unblocked Swift / Kotlin / Ruby / PHP / C# that had been silently skipped for months.

Tier	Languages
Full index + symbol + call graph	Python · Java · JavaScript · TypeScript · Go · Rust · C · C++ · C# · Swift · Kotlin · Ruby · PHP
Full index + symbols (call-graph wiring pending)	Bash · Scala
Single-file analysis (CLI)	HTML · CSS · Markdown · SQL · YAML
Scaffold (plugin exists, indexer wiring pending)	json

CodeGraph supports a similar set. Dart, Vue, Svelte, Lua are not yet shipped — aspirational backlog, no committed date.

---

Configuration

Mostly nothing. The defaults are designed so you can hook it into your agent and forget:

• Output format: TOON. Override per-call with output_format: "json".
• Project root: TREE_SITTER_PROJECT_ROOT (env var, MCP) or --project-root (CLI).
• Cache location: <project>/.ast-cache/. Safe to delete — auto-rebuilds.
• Optional: TREE_SITTER_OUTPUT_PATH for large-output write target.

---

Quality & Testing

Metric	Value
Tests passed	18,493 ✅
Coverage
Type safety	100 % mypy
Platforms	macOS · Linux · Windows
Pre-commit gates	ruff · bandit · mypy · pyupgrade · detect-secrets · tsa-codemap-sync

uv run pytest -q                                # full suite
uv run pytest -q --maxfail=1 -m "not slow and not full_language and not integration"  # fast local loop
PYTEST_XDIST_AUTO_NUM_WORKERS=1 uv run pytest -q --maxfail=1 -m "not slow and not full_language and not integration"  # one-worker mode for lower CPU load
PYTEST_XDIST_AUTO_NUM_WORKERS=2 uv run pytest -q --maxfail=1 -m "not slow and not full_language and not integration"  # two-worker balanced mode
uv run pytest --lf --maxfail=1                  # rerun only failed tests from last run
uv run python check_quality.py --new-code-only  # quality gate

---

Troubleshooting

Symptom	Fix
unsupported language on .swift / .kt / .rb / .php / .cs	Update to ≥ 1.12.x — the 5-language gap was patched in commit 50e99a8f. Grammar modules for extras-gated languages are not bundled in the base install; run pip install "tree-sitter-analyzer[swift]" (or kotlin, ruby, php, csharp) to add them.
MCP server doesn't appear in client	TREE_SITTER_PROJECT_ROOT must be absolute; restart the client after config edit.
database is locked	Stop any other process holding .ast-cache/index.db; if persistent, rm -rf .ast-cache && tree-sitter-analyzer --autoindex.
Slow first call	First call builds the index. Subsequent calls are sub-second. Run --full-index upfront to amortise.
Agent picks the wrong tool	Use a tsa-* skill (/tsa-graph, /tsa-find, ...) — each skill restricts the visible tool set to one workflow.

---

Development

git clone https://github.com/aimasteracc/tree-sitter-analyzer.git
cd tree-sitter-analyzer
uv sync --extra all --extra mcp
uv run pytest -q

See docs/CONTRIBUTING.md for the development guide.

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Contributing & License

• ⭐ A GitHub star helps surface this tool to other AI-agent users.
• 💖 Sponsor — supports continued MCP / Skills development.
• Lead sponsor: @o93.
• MIT licensed — see LICENSE.
• Release history: CHANGELOG.md.