pip install nexus-mcp-ci
claude mcp add nexus-mcp-ci -- nexus-mcp-ci

# 1. Install
pip install nexus-mcp-ci

# 2. Register with Claude Code
claude mcp add nexus-mcp-ci -- nexus-mcp-ci

# 3. Verify (in any Claude Code session)
# Claude will automatically use nexus-mcp-ci tools when CLAUDE.md instructs it

## Code Navigation

Use nexus-mcp-ci tools before built-in file tools:
- Start sessions with `mcp__nexus-mcp__status`; run `index` if needed
- `search` before `Read/Grep`
- `explain` instead of reading a file to understand a symbol
- `impact` before any refactor

Source files
    │
    ├─ Step 1: Discover ──────── walk tree, filter by ext/size/.gitignore
    │
    ├─ Step 2: Parse symbols ─── tree-sitter (parallel ThreadPool)
    │           extracts: functions, classes, methods
    │           captures: name, signature, docstring, line_start/end, language
    │
    ├─ Step 3: Parse graph ────── ast-grep (sequential for consistency)
    │           extracts: call edges, import edges, inheritance edges
    │           output: UniversalGraph(nodes=[], edges=[])
    │
    ├─ Step 4: Transfer graph ── populate rustworkx PyDiGraph
    │           O(1) node lookup by name, Rust-backed traversal
    │
    ├─ Step 5: Chunk ──────────── Symbol → CodeChunk
    │           deterministic IDs: SHA256(file_path + symbol_name + line)
    │           avoids duplicate inserts on incremental reindex
    │
    ├─ Step 6: Embed ──────────── bge-small-en: 384-dim (default) or jina-code: 768-dim via ONNX
    │           lazy-loaded, unloaded after indexing (try/finally)
    │           GPU/MPS auto-detected; falls back to CPU
    │
    ├─ Step 7: Store ──────────── write to LanceDB `chunks` table (12-col PyArrow schema)
    │           rebuild native FTS (Tantivy) index after write
    │
    └─ Step 8: Cleanup ────────── unload model, persist metadata (mtimes for incremental)
                                  save rustworkx graph to SQLite (warm-start recovery)

search("how does auth work")
         │
         ├─► vector_engine.search(query, n=30)  ← cosine similarity on 768-dim embeddings
         │                                         "auth" finds "verify_credentials", "token_check"
         │
         ├─► bm25_engine.search(query, n=30)    ← Tantivy FTS on same LanceDB table
         │                                         fast exact-keyword matching
         │
         ├─► graph_engine.boost(query, n=30)    ← structural relevance score
         │                                         hub symbols (high in/out degree) boosted
         │
         └─► fusion.merge(v_results, b_results, g_results)
                  │
                  │  Reciprocal Rank Fusion: score = Σ weight_i / (k + rank_i)
                  │  default weights: vector=0.5, bm25=0.3, graph=0.2
                  │
                  ├─► reranker.rerank(top_20)   ← FlashRank (optional, 4MB ONNX model, <10ms)
                  │
                  └─► token_budget.truncate()   ← summary / detailed / full
                           │
                           └─► Top-N chunks, scored, formatted

pip install nexus-mcp-ci

# GPU (CUDA) support — adds ONNX CUDA execution provider
pip install nexus-mcp-ci[gpu]

# FlashRank reranker — adds ~4MB cross-encoder for better search quality
pip install nexus-mcp-ci[reranker]

# Both
pip install nexus-mcp-ci[gpu,reranker]

git clone https://github.com/jaggernaut007/Nexus-MCP.git
cd Nexus-MCP
./setup.sh           # creates venv, installs, verifies
# or
pip install -e ".[dev]"

# Minimal
claude mcp add nexus-mcp-ci -- nexus-mcp-ci

# With the code-specific embedding model (requires trust_remote_code)
claude mcp add nexus-mcp-ci -e NEXUS_EMBEDDING_MODEL=jina-code -- nexus-mcp-ci

# GPU embeddings
claude mcp add nexus-mcp-ci -e NEXUS_EMBEDDING_DEVICE=cuda -- nexus-mcp-ci

# Virtualenv install — pass the full binary path
claude mcp add nexus-mcp-ci -- /path/to/.venv/bin/nexus-mcp-ci

{
  "mcpServers": {
    "nexus-mcp-ci": {
      "command": "nexus-mcp-ci",
      "args": [],
      "env": {
        "NEXUS_EMBEDDING_MODEL": "jina-code"
      }
    }
  }
}

{
  "nexus-mcp-ci": {
    "command": "nexus-mcp-ci",
    "transport": "stdio"
  }
}

## Code Intelligence — nexus-mcp-ci

Every code task in this project MUST follow this workflow:

1. **Session start**: `mcp__nexus-mcp__status` → if not indexed, `mcp__nexus-mcp__index`
2. **Before any file read**: `mcp__nexus-mcp__search` to locate relevant code
3. **To understand a symbol**: `mcp__nexus-mcp__explain` (not Read)
4. **Before refactoring**: `mcp__nexus-mcp__impact` to assess blast radius
5. **For project orientation**: `mcp__nexus-mcp__overview` or `mcp__nexus-mcp__architecture`

# Session start
status()               → "indexed: True, 8,412 chunks, 1,203 symbols, 87 MB"

# Code discovery
search("JWT token validation", mode="hybrid", n=10)
  → auth/jwt.py:42  validate_token()         score=0.94
  → auth/middleware.py:18  require_auth()    score=0.87
  → tests/test_auth.py:91  test_valid_jwt()  score=0.81

# Deep symbol understanding
explain("validate_token")
  → definition, docstring, params, complexity
  → callers: [require_auth, login_required, api_key_check]
  → callees: [decode_jwt, check_expiry, verify_signature]
  → quality: complexity=6, smells=[], maintainability=A

# Pre-refactor safety check
impact("validate_token")
  → direct callers: 3 symbols
  → transitive impact: 12 symbols across 4 files
  → high-risk: auth/middleware.py (5 dependents)

# Index multiple roots in one call — processed sequentially, shared engines
index(path="packages/api/src,packages/shared/src,packages/cli/src")

# Or use the paths parameter for additional roots
index(path="packages/api/src", paths="packages/shared/src,packages/cli/src")

git clone https://github.com/jaggernaut007/Nexus-MCP.git
cd Nexus-MCP
pip install -e ".[dev]"

pytest -v                    # 441 tests
pytest -m "not slow"         # skip performance benchmarks
pytest tests/test_search.py  # single module
ruff check .                 # lint

src/nexus_mcp/
├── server.py              # FastMCP entrypoint — 10 tools, input validation, graceful shutdown
├── config.py              # Settings (NEXUS_ env prefix)
├── state.py               # Global singleton SessionState
├── core/
│   ├── models.py          # Symbol, ParsedFile, CodebaseIndex, Memory
│   ├── graph_models.py    # UniversalNode, Relationship
│   ├── interfaces.py      # IParser, IEngine protocols
│   └── exceptions.py      # NexusException hierarchy
├── parsing/
│   ├── treesitter_parser.py   # Symbol extraction (parallel)
│   ├── astgrep_parser.py      # Structural graph extraction (sequential)
│   ├── language_registry.py   # 25+ language definitions
│   └── file_watcher.py        # Debounced watchdog for live reindex
├── engines/
│   ├── vector_engine.py   # LanceDB cosine similarity search
│   ├── bm25_engine.py     # LanceDB native FTS (Tantivy)
│   ├── graph_engine.py    # rustworkx PyDiGraph with RLock
│   ├── fusion.py          # Reciprocal Rank Fusion
│   └── reranker.py        # FlashRank (optional, graceful degradation)
├── indexing/
│   ├── pipeline.py        # 8-step indexing pipeline
│   ├── embedding_service.py   # ONNX Runtime, GPU/MPS auto-detect
│   ├── parallel_indexer.py    # ThreadPool over files
│   └── chunker.py         # Symbol → CodeChunk with deterministic IDs
├── memory/
│   └── memory_store.py    # LanceDB-backed memory, TTL, 6 types
├── analysis/
│   └── code_analyzer.py   # Cyclomatic/cognitive complexity, smells
├── security/
│   ├── permissions.py     # READ/MUTATE/WRITE tool categories
│   └── rate_limiter.py    # Token-bucket, per-tool, thread-safe
└── middleware/
    └── audit.py           # Structured audit logs, correlation IDs, field redaction

python self_test/demo_mcp.py                   # built-in sample project
python self_test/demo_mcp.py /path/to/project  # your own codebase