diff --git a/api/mcp/__init__.py b/api/mcp/__init__.py
new file mode 100644
index 00000000..c161c8e1
--- /dev/null
+++ b/api/mcp/__init__.py
@@ -0,0 +1,8 @@
+"""MCP server module for code-graph.
+
+Exposes the code-graph indexer and graph queries as MCP tools so AI coding
+agents (Claude Code, Cursor, Copilot, Roo/Cline) can drive the indexer over
+the standard Model Context Protocol stdio transport.
+
+Entry point: ``cgraph-mcp`` (defined in ``pyproject.toml``).
+"""
diff --git a/api/mcp/server.py b/api/mcp/server.py
new file mode 100644
index 00000000..d81111df
--- /dev/null
+++ b/api/mcp/server.py
@@ -0,0 +1,26 @@
+"""FastMCP server for code-graph.
+
+This is the scaffold (T1). It instantiates a single FastMCP app, exposes it
+as ``app`` for tests and embedders, and registers a ``main()`` entry point
+that runs the server over stdio. Tools are registered in later tickets
+(T4-T8, T11) by importing this module's ``app`` and decorating functions
+with ``@app.tool(...)``.
+"""
+
+from __future__ import annotations
+
+from mcp.server.fastmcp import FastMCP
+
+app: FastMCP = FastMCP("code-graph")
+
+
+def main() -> None:
+    """Run the MCP server over stdio.
+
+    Console-script entry point for ``cgraph-mcp``.
+    """
+    app.run()
+
+
+if __name__ == "__main__":
+    main()
diff --git a/docs/MCP_SERVER_DESIGN.md b/docs/MCP_SERVER_DESIGN.md
new file mode 100644
index 00000000..38b2f077
--- /dev/null
+++ b/docs/MCP_SERVER_DESIGN.md
@@ -0,0 +1,321 @@
+# Code Graph MCP Server — Design Summary
+
+## What We're Building
+
+An MCP server inside the `code-graph` repo that gives AI coding agents two capabilities:
+1. **Structural tools** (deterministic, no LLM): get_callers, get_callees, get_dependencies, impact_analysis, find_path, search_code, index_repo
+2. **Ask tool** (GraphRAG SDK, needs LLM): natural language questions about the codebase → NL-to-Cypher → grounded answers
+
+Phase 1 also bundles three foundational improvements to `api/` that the MCP server needs and that benefit all consumers of code-graph (CLI, web UI, future integrations):
+
+3. **Multi-branch graph identity**: per `(repo, branch)` graph naming so concurrent agents on different branches can't corrupt each other's view. (Today, two users on different branches overwrite each other's graphs — this is a real bug.)
+4. **Incremental indexing**: file-hash-based skip-unchanged so agents can call `index_repo` cheaply on every interaction. Default-on once a graph exists.
+5. **Tree-sitter language expansion**: a shared `TreeSitterAnalyzer` base class plus 5 new languages (Go, Rust, TypeScript, Ruby, C++) and re-enabling C. Brings supported languages from 5 to 11.
+
+## Key Decisions Made
+
+- **Mono-repo**: Build inside `code-graph/api/mcp/`, not a separate project. One pip package, one repo.
+- **Module path is `api/mcp/`, NOT top-level `mcp/`**: A top-level `mcp/` directory would shadow the installed `mcp` PyPI SDK and break `from mcp.server.fastmcp import FastMCP`. Entry point: `cgraph-mcp = "api.mcp.server:main"`.
+- **Python MCP server**: Use the official `mcp` Python SDK (`from mcp.server.fastmcp import FastMCP`), NOT standalone `fastmcp` or Node.js. Avoids language bridge.
+- **Reuse everything**: Most code already exists. The MCP tools are thin wrappers around `api/graph.py`, `api/project.py`, `api/cli.py`, and `api/llm.py`.
+- **GraphRAG SDK powers the ask tool**: `kg.ask()` does NL-to-Cypher. Code-graph's `api/llm.py` already integrates this — repackage for MCP.
+- **Reuse the existing hand-coded ontology** from `api/llm.py:_define_ontology()` (lines 26–233) rather than auto-extracting via `Ontology.from_kg_graph()`. The hand-coded version has richer entity attributes and descriptions tuned for code. Refactor: rename `_define_ontology` → `define_ontology` so the MCP module can import it.
+- **11 languages in Phase 1**: Python/JS/Kotlin via tree-sitter (refactored onto a shared base class in T15), Go/Rust/TypeScript/Ruby/C/C++ added in T16, Java/C# stay on multilspy.
+- **Incremental indexing in Phase 1**: file-hash-based skip-unchanged, default-on once a `(project, branch)` graph exists (T18). Full re-index via `--full` (CLI) or `incremental=False` (MCP).
+- **No Graphiti/memory or raw FalkorDB MCP in v1**: Out of scope. Available as separate servers. Architecture supports merging later.
+- **Auto-init for zero config**: ensure-db auto-starts FalkorDB Docker, auto-index on first tool call, auto-GraphRAG init.
+- **Expose Cypher in ask responses**: Transparency for the agent + learning patterns.
+- **Stdio transport only in Phase 1**: HTTP/SSE deferred to Phase 1.5. Stdio is sufficient for Claude Code, Cursor, and Claude Desktop.
+- **`impact_analysis` defaults**: direction `IN` (upstream callers — "what breaks if I change this"), depth `3`, max depth clamp `10`. Parameters allow override.
+- **Multi-branch graph identity**: graph name is `code:{project}:{branch}`. Sourcegraph-zoekt-style isolation. The IDE/LSP "single current index, re-index on switch" model only works because IDEs are single-tenant; code-graph is multi-tenant (a server, not a desktop tool, with concurrent agents on different branches), so per-branch isolation is required for correctness. Existing single-graph deployments migrate to `code:{project}:_default`. Within a branch, the existing transition-based `switch_commit` flow continues to work unchanged.
+- **`index_repo` auto-detects branch**: from `git rev-parse --abbrev-ref HEAD` in the target path. Optional override parameter. Non-git paths use `_default`.
+- **Incremental indexing default-on**: once a `(project, branch)` graph exists, `index_repo` and `cgraph index` auto-detect and run incremental. Opt out with `--full` (CLI) or `incremental=False` (MCP). First-time runs are full. Tracks per-file SHA256 hashes in Redis under `{repo}:{branch}_files`. Built on the existing `delete_files()` primitive in `api/graph.py` (today only used in the git-history flow).
+- **Tree-sitter base class**: refactor existing PythonAnalyzer / JavaScriptAnalyzer / KotlinAnalyzer onto a shared `TreeSitterAnalyzer` base in Phase 1. Five new languages added on the new base in the same phase. C is re-enabled. Java and C# stay on multilspy (LSP) until a future phase.
+
+## Directory Structure
+
+```text
+code-graph/
+├── api/                          # Existing Python backend (FastAPI, analyzers, graph, llm, cli)
+│   └── mcp/                      # NEW — MCP server module (under api/ to avoid shadowing the installed `mcp` SDK)
+│       ├── __init__.py
+│       ├── server.py             # FastMCP entry point, tool registration, stdio transport
+│       ├── auto_init.py          # ensure-db + auto-index hooks
+│       ├── graphrag_init.py      # KnowledgeGraph construction + per-project caching (reuses api/llm.py:define_ontology)
+│       ├── code_prompts.py       # Re-exports + hooks for GraphRAG prompts (sourced from api/prompts.py)
+│       ├── templates/            # Agent guidance file templates (cursorrules, claude_mcp_section)
+│       └── tools/
+│           ├── __init__.py
+│           ├── structural.py     # index_repo, get_callers, get_callees, get_dependencies,
+│           │                     # impact_analysis, find_path, search_code
+│           └── ask.py            # GraphRAG-powered ask tool
+├── app/                          # Existing React frontend
+├── skills/                       # Existing Claude Code skill
+├── tests/
+│   └── mcp/
+│       ├── __init__.py
+│       ├── conftest.py           # Session-scoped FalkorDB + indexed-fixture fixtures
+│       ├── fixtures/
+│       │   ├── sample_project/   # Py/Java/C# fixture with known call graph
+│       │   └── expected.yaml     # Assertion contract: counts, callers, callees, paths, search hits
+│       ├── test_scaffold.py      # Scaffold smoke test (T1)
+│       ├── test_index_repo.py    # T4 — unit + integration + protocol
+│       ├── test_neighbors.py     # T5 — unit + integration + protocol + CLI parity
+│       ├── test_impact_analysis.py # T6
+│       ├── test_find_path.py     # T7
+│       ├── test_search_code.py   # T8
+│       ├── test_graphrag_init.py # T9
+│       ├── test_code_prompts.py  # T10 (snapshot)
+│       ├── test_ask.py           # T11 — mocked LLM, real Cypher against fixture
+│       ├── test_auto_init.py     # T12
+│       └── test_init_agent.py    # T13
+└── pyproject.toml                # Adds `cgraph-mcp = "api.mcp.server:main"` and `mcp>=1.0,<2.0`
+```
+
+**Note on test layout:** Each tool ticket ships its own integration + MCP-protocol round-trip tests in the same PR — there is no separate "integration tests" or "protocol tests" milestone. The previous `integration/` and `e2e/` subdirectories are removed in favor of per-tool test files. Real-LLM E2E is deferred to Phase 1.5.
+
+## CLI-to-MCP Tool Mapping
+
+| cgraph Command | MCP Tool | Shared Code | Delta |
+|---|---|---|---|
+| `cgraph index` / `index-repo` | `index_repo` | api/project.py, analyzers/ | + GraphRAG init after indexing |
+| `cgraph neighbors --rel CALLS --dir in` | `get_callers` | api/graph.py Cypher | Thin wrapper |
+| `cgraph neighbors --rel CALLS --dir out` | `get_callees` | api/graph.py Cypher | Thin wrapper |
+| `cgraph neighbors` (multi-rel) | `get_dependencies` | api/graph.py Cypher | New multi-rel query |
+| (new) | `impact_analysis` | api/graph.py Cypher | New variable-depth traversal |
+| `cgraph paths` | `find_path` | api/graph.py Cypher | Thin wrapper |
+| `cgraph search` | `search_code` | api/auto_complete.py | Thin wrapper |
+| (web UI chat) | `ask` | api/llm.py + GraphRAG SDK | Repackage as MCP tool |
+
+## GraphRAG SDK Integration Pattern
+
+The MCP `ask` tool is a thin wrapper around the GraphRAG SDK flow already implemented in `api/llm.py`. End-to-end:
+
+1. **Pre-step (once per project, in `api/mcp/graphrag_init.py`):** construct a `KnowledgeGraph` and cache it. Reuses the existing hand-coded ontology from `api/llm.py:define_ontology()` (renamed from `_define_ontology` in T9).
+
+2. **Per-call (in the `ask` tool):** retrieve cached `KnowledgeGraph`, call `kg.ask(question)`, return `{answer, cypher_query, context_nodes}`. Internally this is **two LLM round-trips bracketing one Cypher query against FalkorDB**:
+   - LLM #1: question + ontology → Cypher
+   - FalkorDB: execute Cypher → rows
+   - LLM #2: question + rows → natural-language answer
+
+   The graph itself never goes to the LLM — only schema and query results — which is why this works on huge codebases.
+
+```python
+# api/mcp/graphrag_init.py — construct once, cache per project
+from graphrag_sdk import KnowledgeGraph
+from graphrag_sdk.models.litellm import LiteModel
+from graphrag_sdk.model_config import KnowledgeGraphModelConfig
+
+from api.llm import define_ontology  # renamed from _define_ontology in T9
+from api.mcp.code_prompts import (
+    CYPHER_GEN_SYSTEM, CYPHER_GEN_PROMPT,
+    GRAPH_QA_SYSTEM, GRAPH_QA_PROMPT,
+)
+
+_kg_cache: dict[str, KnowledgeGraph] = {}
+
+def get_or_create_kg(project_name: str) -> KnowledgeGraph:
+    if project_name in _kg_cache:
+        return _kg_cache[project_name]
+
+    model = LiteModel(model_name=os.getenv("MODEL_NAME", "gemini/gemini-flash-lite-latest"))
+    kg = KnowledgeGraph(
+        name=f"code:{project_name}",
+        model_config=KnowledgeGraphModelConfig.with_model(model),
+        ontology=define_ontology(),                    # REUSE — do NOT call Ontology.from_kg_graph
+        cypher_system_instruction=CYPHER_GEN_SYSTEM,
+        qa_system_instruction=GRAPH_QA_SYSTEM,
+        cypher_gen_prompt=CYPHER_GEN_PROMPT,
+        qa_prompt=GRAPH_QA_PROMPT,
+    )
+    _kg_cache[project_name] = kg
+    return kg
+
+# api/mcp/tools/ask.py — the tool itself
+async def ask(question: str) -> dict:
+    kg = get_or_create_kg(current_project_name())
+    response = await asyncio.get_event_loop().run_in_executor(None, kg.ask, question)
+    return {
+        "answer": response.answer,
+        "cypher_query": response.cypher_query,   # exposed for transparency
+        "context_nodes": response.context_nodes,
+    }
+```
+
+## Multi-Branch Graph Identity
+
+**Problem.** Today, `Graph(project_name)` (api/project.py:225, api/index.py:246) names every graph after the repo directory. There is no branch component. Two users (or agents) indexing the same repo on different branches **silently overwrite each other** — the second indexer wipes the first. The Redis metadata under `{repo}_info` (api/info.py:33-46) is also a single global hash per repo, so the commit pointer is shared. This is a real bug that the MCP server will hit immediately because agents working on PR branches need their branch's view, not stale state from someone else's main.
+
+**Comparison with prior art.**
+
+| System | Storage | Branch behavior | Why it works for them |
+|---|---|---|---|
+| JetBrains IDEs | Single on-disk index | Filesystem-state-based; re-index on `git checkout` | Single-tenant; one developer, one workspace |
+| VS Code + LSPs | In-memory per workspace + content-hash cache | LSP receives `didChangeWatchedFiles`, reanalyzes touched files | Single-tenant; each workspace is isolated by process |
+| GitHub Blackbird | Server-side, commit-sharded, deduped | All commits indexed simultaneously | Massive scale; full historical search |
+| Sourcegraph zoekt | Per `(repo, branch)` shard | Default branch always indexed; others by config | Server, multi-tenant, interactive use |
+| Sourcegraph SCIP | Per-commit graph data uploaded by CI | Commit-keyed | Reproducible cross-commit code intel |
+
+Code-graph is architecturally a server (FalkorDB-backed, accessed by multiple clients), so the IDE single-index model is wrong for it. The closest analog is **Sourcegraph zoekt: per `(repo, branch)` graphs**.
+
+**Solution (T17).** Graph naming becomes `code:{project_name}:{branch}`. The full set of changes:
+
+| File | Change |
+|---|---|
+| `api/graph.py` | `Graph` and `AsyncGraphQuery` constructors take a `branch` parameter; default `_default`; graph name composed as `code:{project}:{branch}` |
+| `api/project.py` | `Project.from_git_repository()` and `Project.from_local_directory()` accept and propagate `branch`; auto-detect via `git rev-parse --abbrev-ref HEAD` when `None` |
+| `api/info.py` | Redis metadata keys become `{repo}:{branch}_info`; `set_repo_commit`, `get_repo_commit`, etc. take a branch param |
+| `api/git_utils/` | Git-transitions graph becomes `{repo}:{branch}_git`; `switch_commit` stays scoped to a single branch graph |
+| `api/cli.py` | `cgraph index --branch <name>`; `cgraph list` enumerates `(project, branch)` pairs; `cgraph info`, `cgraph search` accept `--branch` |
+| `api/index.py` | `/api/list_repos`, `/api/graph_entities`, `/api/repo_info`, `/api/get_neighbors`, `/api/find_paths`, `/api/auto_complete` accept optional `branch` query param; responses include the branch |
+| MCP `index_repo` | Accepts optional `branch`; auto-detects from target path's checkout; returns `branch` in response |
+
+**Migration.** A one-shot helper renames `code:{project}` → `code:{project}:_default` and copies `{repo}_info` → `{repo}:_default_info` on first read. Documented as `cgraph migrate` for explicit invocation.
+
+**Out of scope for Phase 1.** Cross-branch query tools, branch comparison, branch garbage collection. Each branch is an isolated graph; users prune via `cgraph delete --branch`.
+
+## Incremental Indexing
+
+**Today.** `SourceAnalyzer.first_pass()` (`api/analyzers/source_analyzer.py:82-121`) re-parses **every supported file** on every index call. There is no per-file hash tracking. The codebase already has the primitives for incremental work — `Graph.delete_files()` (referenced in `api/git_utils/git_utils.py:153, 217`) and the file-classification logic in `classify_changes` — but they're coupled to the git-history-build flow and not used for ad-hoc reindexing.
+
+**Solution (T18).** Add file-hash-based incremental indexing on top of T17's per-branch storage. Flow:
+
+1. **Hash store**: Redis hash `{repo}:{branch}_files` mapping `file_path → SHA256(content)`. Persisted at the end of every full or incremental index.
+2. **Diff phase**: `Project.analyze_sources(incremental=True)` walks the file tree, computes current hashes, diffs against the stored map:
+   - **Unchanged** → skip the analyzer entirely
+   - **Modified** → call `delete_files([path])` to remove old graph entities, then re-run the analyzer (first pass) on the file
+   - **Deleted** → call `delete_files([path])` only
+   - **New** → analyze normally
+3. **Second-pass (LSP) decision**: if any file changed, run the LSP-based second pass over the entire branch graph. Per-file second-pass is a Phase 2 optimization (correctness over speed in v1).
+4. **Persist** the new hash map.
+
+**Defaults.**
+- First run on a fresh `(project, branch)` → automatically falls back to full
+- Hash store missing or corrupted → falls back to full with a warning logged
+- File renames → treated as delete + add (rename detection deferred to Phase 2)
+- CLI `cgraph index .` defaults to incremental when a graph exists; `--full` forces full
+- MCP `index_repo` defaults to incremental; response includes `mode: "full"|"incremental"` and `files_changed: list[str]`
+
+**Why this is the right primitive for agents.** Agents call `index_repo` reflexively at the start of every interaction to ensure freshness. With full re-index, this is too slow to be reflexive. With incremental + content-hash skipping (the same trick LSP servers use), the steady-state cost is "diff a few file hashes" — acceptable for every-call use.
+
+## Competitive Context
+
+5 competitors exist: codebase-memory-mcp (66 langs, SQLite), GitNexus (23.8K stars, KuzuDB), Codegraph (11 langs, 30+ tools, SQLite), CodeGraphContext (Neo4j), Code Pathfinder (Python only).
+
+**All share 3 gaps FalkorDB fills:**
+1. No NL query layer (none have an "ask" tool — GraphRAG SDK is the differentiator)
+2. Local-only embedded storage (all SQLite — FalkorDB is client-server, supports shared/team/cloud)
+3. No ecosystem path to memory/intelligence (FalkorDB has Graphiti, GraphRAG SDK, mcpserver)
+
+**Don't compete on:** tool count or language count.
+**Compete on:** ask tool (understanding), shared graphs (scale), cloud path (enterprise).
+
+## CI Testing Strategy
+
+**Each tool ticket ships its own four kinds of tests in the same PR.** No bulk-testing milestones at the end.
+
+| Layer | Runs On | FalkorDB | LLM | What It Tests |
+|---|---|---|---|---|
+| Unit tests | Every PR | Mocked | No | Parameter parsing, Cypher generation, output formatting, error handling |
+| Integration (structural) | Every PR | Docker service | No | Tool against indexed fixture, asserted via `expected.yaml` contract |
+| Integration (ask, mocked) | Every PR | Docker service | Mocked | GraphRAG init, prompt construction, real Cypher execution against fixture, answer formatting |
+| MCP protocol round-trip | Every PR | Docker service | No | `session.list_tools()` schema check + `session.call_tool(...)` round-trip via the `mcp` SDK's stdio client |
+| CLI parity (where applicable) | Every PR | Docker service | No | MCP tool output matches the equivalent `cgraph` CLI command output |
+| E2E (ask, real LLM) | **Phase 1.5** (nightly, deferred) | Docker service | Real (secret) | Prompt quality, answer grounding, regression detection |
+
+GitHub Actions FalkorDB service (added in T2):
+```yaml
+services:
+  falkordb:
+    image: falkordb/falkordb:latest
+    ports:
+      - 6379:6379
+    options: >-
+      --health-cmd "redis-cli ping"
+      --health-interval 10s
+      --health-timeout 5s
+      --health-retries 5
+```
+
+## GitHub Issues Breakdown (Phase 1: 18 vertical issues)
+
+Each tool ticket ships impl + unit + integration + protocol round-trip in a single PR. There are no separate "testing" milestones — testing is folded into every ticket.
+
+### Foundation
+1. **T1 — Scaffold `api/mcp/` module + `cgraph-mcp` entry point.** FastMCP server, stdio runner, `mcp>=1.0,<2.0` dep, copy design doc into repo, scaffold smoke test.
+2. **T2 — CI workflow with FalkorDB service.** `.github/workflows/mcp-tests.yml`, FalkorDB service container, runs on path filter, scaffold smoke test green.
+3. **T3 — Test fixture project + assertion contract.** `tests/mcp/fixtures/sample_project/` with known call graph in Py/Java/C#, plus `expected.yaml` and session-scoped `conftest.py`.
+
+### Core `api/` improvements (prerequisite to MCP tools)
+17. **T17 — Per-branch graph identity.** `code:{project}:{branch}` naming everywhere; branch param on `Graph`, `Project`, `info`, CLI, REST endpoints; one-shot migration helper to `_default`. **On the critical path before T4.**
+18. **T18 — Incremental indexing.** File-hash-based skip-unchanged in `SourceAnalyzer`, default-on once a graph exists. Builds on T17. CLI `--full` flag; MCP `incremental` parameter.
+
+### Structural Tools (each ticket: impl + unit + integration + protocol round-trip + CLI parity)
+4. **T4 — `index_repo` tool.** Wraps `Project.from_git_repository` + `analyze_sources` post-T17. Auto-detects branch; supports incremental via T18.
+5. **T5 — `get_callers` / `get_callees` / `get_dependencies` tools.** Three tools sharing one helper over `AsyncGraphQuery.get_neighbors`.
+6. **T6 — `impact_analysis` tool.** New variable-depth Cypher in `api/graph.py`. Defaults: direction `IN`, depth `3`, max clamp `10`.
+7. **T7 — `find_path` tool.** Wraps `AsyncGraphQuery.find_paths`.
+8. **T8 — `search_code` tool.** Wraps `AsyncGraphQuery.prefix_search`.
+
+### Ask Tool + GraphRAG
+9. **T9 — GraphRAG init module (`api/mcp/graphrag_init.py`).** Reuses `api/llm.py:define_ontology` (renamed from `_define_ontology`). Caches `KnowledgeGraph` per `(project, branch)`.
+10. **T10 — Code-specific prompt overrides (`api/mcp/code_prompts.py`).** Re-exports + snapshot-pinned prompts from `api/prompts.py`.
+11. **T11 — `ask` MCP tool.** Returns `{answer, cypher_query, context_nodes}`. Mocked-LLM integration test executes real Cypher against the T3 fixture.
+
+### Operational
+12. **T12 — Auto-init: ensure FalkorDB + auto-index CWD.** Bootstraps Docker if FalkorDB unreachable; lazy auto-index gated on `CODE_GRAPH_AUTO_INDEX=true`.
+13. **T13 — Agent guidance bundle.** AGENTS.md section, `.cursorrules` template, `cgraph init-agent` CLI command.
+14. **T14 — Packaging.** Dockerfile MCP mode, docker-compose for FalkorDB + MCP server, README quickstart with `claude mcp add-json` snippet.
+
+### Tree-sitter expansion (parallel swimlane)
+15. **T15 — Tree-sitter analyzer base class refactor.** Extract `TreeSitterAnalyzer` base from existing Python/JS/Kotlin analyzers. Strictly non-functional.
+16. **T16 — Add 5 new tree-sitter languages + re-enable C.** Go, Rust, TypeScript, Ruby, C++; per-language fixtures and tests. Brings supported languages from 5 to 11.
+
+### Deferred to Phase 1.5
+- HTTP/SSE transport (was Phase 1 issue #3 in earlier draft)
+- Real-LLM nightly E2E with API-key secrets (was a row in the CI table)
+
+### Dependency graph
+```text
+T1 ──┬─> T2 ──> T3 ──> T17 ──> T4 ──┬─> T5
+     │                                ├─> T6
+     │                                ├─> T7
+     │                                └─> T8
+     ├─> T9 ──> T10 ──> T11 (also needs T3, T17)
+     ├─> T12 (also needs T4)
+     ├─> T13
+     ├─> T14 (also needs T12)
+     ├─> T15 ──> T16
+     └─> T18 (also needs T17, lands in parallel with T4+)
+```
+After T17 lands, multiple streams parallelize: structural tools (T4 → T5/T6/T7/T8), ask (T9 → T10 → T11), tree-sitter expansion (T15 → T16), and incremental indexing (T18). T17 is the only addition to the critical path; everything else is parallel work.
+
+## Configuration
+
+| Variable | Description | Default |
+|---|---|---|
+| FALKORDB_HOST | FalkorDB hostname | localhost |
+| FALKORDB_PORT | FalkorDB port | 6379 |
+| MODEL_NAME | LLM for ask tool (LiteLLM format) | openai/gpt-4o-mini |
+| LLM_API_KEY | API key for ask tool (optional) | — |
+| CODE_GRAPH_AUTO_INDEX | Auto-index on first tool call | false |
+| CODE_GRAPH_IGNORE | Dirs to ignore | node_modules,.git,__pycache__ |
+| MCP_TRANSPORT | stdio or http | stdio |
+| MCP_PORT | HTTP transport port | 3000 |
+
+Quick start (Claude Code):
+```bash
+claude mcp add-json "code-graph" '{"command":"cgraph-mcp","env":{"FALKORDB_HOST":"localhost","LLM_API_KEY":"sk-..."}}'
+```
+
+## Roadmap
+
+- **Phase 1:** MCP server with 8 tools. **11 languages** (Python/JS/Kotlin/Go/Rust/TypeScript/Ruby/C/C++ via tree-sitter; Java/C# via multilspy). Stdio transport. Auto-init. Agent guidance. **Per-branch graph identity. Default-on incremental indexing.** **18 vertical issues** (T1–T18).
+- **Phase 1.5:** HTTP/SSE transport. Real-LLM nightly E2E with secret-managed API key. Prompt iteration on `ask` tool.
+- **Phase 2:** Cross-branch query tools ("what changed between branches"). Per-file second-pass LSP optimization in incremental indexing. Rename detection in incremental flow. tree-sitter language coverage beyond the 11 (toward the 60+ baseline). Benchmarks.
+- **Phase 3:** Dedicated TS/Go analyzers (replacing tree-sitter for those two with deeper LSP integration). Copilot extension. FalkorDB Cloud integration. Branch garbage collection / TTL.
+- **Future:** Merge with Graphiti (memory) and mcpserver (raw graph) into unified `@falkordb/code-intelligence`.
+
+## Design Doc
+
+The full design document (v4) is in `code-graph-mcp-v4.docx` and covers: competitive landscape, architecture, tool catalog, data model, parsing strategy, GraphRAG integration, agent integration patterns, current state assessment, execution roadmap, success metrics, risks, and configuration reference.
diff --git a/docs/code-graph-mcp-v4.docx b/docs/code-graph-mcp-v4.docx
new file mode 100644
index 00000000..5b1064b6
Binary files /dev/null and b/docs/code-graph-mcp-v4.docx differ
diff --git a/pyproject.toml b/pyproject.toml
index 121c5b9f..95eb07d7 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -23,10 +23,12 @@ dependencies = [
     "javatools>=1.6.0,<2.0.0",
     "pygit2>=1.17.0,<2.0.0",
     "typer>=0.24.0,<1.0.0",
+    "mcp>=1.0.0,<2.0.0",
 ]
 
 [project.scripts]
 cgraph = "api.cli:app"
+cgraph-mcp = "api.mcp.server:main"
 
 [project.optional-dependencies]
 test = [
diff --git a/tests/mcp/__init__.py b/tests/mcp/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/tests/mcp/test_scaffold.py b/tests/mcp/test_scaffold.py
new file mode 100644
index 00000000..72bb8d05
--- /dev/null
+++ b/tests/mcp/test_scaffold.py
@@ -0,0 +1,59 @@
+"""Scaffold smoke tests for the cgraph-mcp server (T1).
+
+These tests prove the bare module is wired correctly:
+
+1. The FastMCP ``app`` instance is importable.
+2. The ``cgraph-mcp`` console script spawns a working stdio MCP server.
+3. A client can complete the MCP handshake and ``list_tools`` returns 0
+   tools (no tools are registered yet — they land in T4-T8, T11).
+
+When tool tickets land they should ADD tests, not modify these — these
+guard the scaffold itself.
+"""
+
+from __future__ import annotations
+
+import shutil
+
+import anyio
+import pytest
+from mcp import ClientSession, StdioServerParameters
+from mcp.client.stdio import stdio_client
+
+STDIO_TIMEOUT = 30  # seconds — prevents CI from hanging if the server fails to start
+
+
+def test_app_is_importable() -> None:
+    """The FastMCP instance can be imported and is named ``code-graph``."""
+    from api.mcp.server import app
+
+    assert app is not None
+    assert app.name == "code-graph"
+
+
+def test_main_entry_point_exists() -> None:
+    """``main()`` is exposed for the console script."""
+    from api.mcp import server
+
+    assert callable(server.main)
+
+
+@pytest.mark.anyio
+async def test_stdio_server_lists_zero_tools() -> None:
+    """Spawn ``cgraph-mcp`` over stdio and verify the protocol handshake.
+
+    The scaffold registers no tools, so ``list_tools`` must return an
+    empty list. Tool tickets (T4-T8, T11) extend this expectation.
+    """
+    cgraph_mcp = shutil.which("cgraph-mcp")
+    assert cgraph_mcp is not None, (
+        "cgraph-mcp not on PATH; run `uv pip install -e .` first"
+    )
+
+    params = StdioServerParameters(command=cgraph_mcp, args=[])
+    with anyio.fail_after(STDIO_TIMEOUT):
+        async with stdio_client(params) as (read, write):
+            async with ClientSession(read, write) as session:
+                await session.initialize()
+                result = await session.list_tools()
+                assert result.tools == []
diff --git a/uv.lock b/uv.lock
index 42d272fd..2f57f302 100644
--- a/uv.lock
+++ b/uv.lock
@@ -256,6 +256,45 @@ wheels = [
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 ]
 
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+version = "46.0.7"
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+]
+
 [[package]]
 name = "ct3"
 version = "3.4.0.post5"
@@ -317,6 +356,7 @@ dependencies = [
     { name = "fastapi" },
     { name = "graphrag-sdk" },
     { name = "javatools" },
+    { name = "mcp" },
     { name = "pygit2" },
     { name = "python-dotenv" },
     { name = "tree-sitter" },
@@ -346,6 +386,7 @@ requires-dist = [
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     { name = "httpx", marker = "extra == 'test'", specifier = ">=0.28.0,<1.0.0" },
     { name = "javatools", specifier = ">=1.6.0,<2.0.0" },
+    { name = "mcp", specifier = ">=1.0.0,<2.0.0" },
     { name = "pygit2", specifier = ">=1.17.0,<2.0.0" },
     { name = "pytest", marker = "extra == 'test'", specifier = ">=9.0.2,<10.0.0" },
     { name = "python-dotenv", specifier = ">=1.0.1,<2.0.0" },
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 ]
 
+[[package]]
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+version = "0.4.3"
+source = { registry = "https://pypi.org/simple" }
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+
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 name = "huggingface-hub"
 version = "1.6.0"
@@ -875,6 +925,31 @@ wheels = [
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+[[package]]
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+version = "1.27.0"
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+    { name = "httpx" },
+    { name = "httpx-sse" },
+    { name = "jsonschema" },
+    { name = "pydantic" },
+    { name = "pydantic-settings" },
+    { name = "pyjwt", extra = ["crypto"] },
+    { name = "python-multipart" },
+    { name = "pywin32", marker = "sys_platform == 'win32'" },
+    { name = "sse-starlette" },
+    { name = "starlette" },
+    { name = "typing-extensions" },
+    { name = "typing-inspection" },
+    { name = "uvicorn", marker = "sys_platform != 'emscripten'" },
+]
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