graph-indexer 1.0.1 → 1.0.3

package/README.md

@@ -1,144 +1,97 @@
 # graph-indexer
 
 <p align="center">
-  <strong>Zero-Database • Air-Gapped • AST-Precise • Hybrid Semantic Search</strong><br>
-  <em>Production-grade MCP code indexer for AI coding agents — surgical context retrieval that cuts token costs by up to 84% and improves code accuracy.</em>
+  <strong>Zero-Database · Air-Gapped · AST-Precise · Hybrid Search</strong><br>
+  <em>An MCP server that lets AI coding agents search your codebase by concept instead of reading files — reducing context usage by 65–88% per query.</em>
 </p>
 
 <p align="center">
   <a href="https://www.npmjs.com/package/graph-indexer"><img src="https://img.shields.io/npm/v/graph-indexer?color=blue&style=flat-square" alt="npm version"></a>
   <a href="LICENSE"><img src="https://img.shields.io/badge/License-MIT-yellow.svg?style=flat-square" alt="License: MIT"></a>
   <a href="https://nodejs.org"><img src="https://img.shields.io/badge/Node.js-%3E%3D18-green?style=flat-square" alt="Node.js 18+"></a>
-  <a href="#test-results"><img src="https://img.shields.io/badge/Recall@5-100%25-brightgreen?style=flat-square" alt="Recall@5 100%"></a>
+  <a href="#results"><img src="https://img.shields.io/badge/Recall@5-100%25-brightgreen?style=flat-square" alt="Recall@5 100%"></a>
 </p>
 
 ---
 
-## The Problem: Token Waste and Lost Context
+## Table of Contents
 
-When you use an AI coding agent (Claude, Cursor, GitHub Copilot) on a real codebase, the default workflow wastes **80–90% of your context window**:
+- [What it does](#what-it-does)
+- [Results](#results)
+- [Getting started](#getting-started)
+- [MCP tools](#mcp-tools)
+- [Configuration](#configuration)
+- [Supported languages](#supported-languages)
+- [How it works](#how-it-works)
+- [Best practices](#best-practices)
+- [Troubleshooting](#troubleshooting)
+- [Development](#development)
+- [License](#license)
 
-```
-Agent wants:  "Find the payment processing function"
-Standard workflow:
-  1. Read file: src/payments/handlers.ts (850 lines) → ~10,625 tokens
-  2. Read file: src/config/stripe.ts (340 lines) → ~4,250 tokens  
-  3. Read file: src/types/payment.ts (120 lines) → ~1,500 tokens
-  Total: ~16,375 tokens to find ONE function worth ~200 tokens ⚠️
-
-Reality for complex refactors:
-  • 5–10 such reads per session
-  • ~80,000–160,000 tokens just for context gathering
-  • At Claude 3.5 Sonnet pricing, that's ~$0.48–$0.96 per refactor
-  • AND the LLM accuracy *decreases* — it gets lost in the noise
-```
+---
 
-Three compounding problems:
+## What it does
 
-1. **Token burn:** File reads consume 10–50× more tokens than necessary
-2. **Lost in the Middle:** LLMs lose accuracy when relevant code is buried in 1000-line files
-3. **Topology blindness:** The agent can't see cross-file dependencies. Refactors break silently.
+graph-indexer pre-indexes your codebase into an AST-precise search index and exposes it as an MCP server. Instead of reading full files, AI agents call `search_code("payment validation")` and get back the exact functions that match — with type signatures, docstrings, dependency graph, and call sites — in a fraction of the tokens.
 
-## The Solution: Surgical, AST-Precise Retrieval
+It runs entirely on your machine. No external database, no cloud APIs, no telemetry.
 
-**graph-indexer** is a local MCP server that replaces file reads with **structural code queries**. Instead of reading entire files, your agent retrieves exactly the code it needs.
+**Token comparison:**
 
 ```
+Agent task: "Add error handling to the payment processing flow"
+
+Without graph-indexer:
+  readFile("src/payments/service.ts")   →  8,400 tokens
+  readFile("src/payments/handlers.ts")  →  6,200 tokens
+  readFile("src/types/payment.ts")      →  1,800 tokens
+  Total:                                ~ 16,400 tokens
+
 With graph-indexer:
-  1. Search: "payment processing" → returns [processPayment, validateCard, chargeCustomer]
-  2. One get_chunk() call → ~300 tokens
-  3. Dependency topology included → can see full call chain
-  Total: ~300 tokens vs ~16,375 tokens — 98% savings on this query
+  search_code("payment processing")     →    650 tokens  (5 exact chunks)
+  get_chunk("chunk_id")                 →    280 tokens  (full function body)
+  Total:                                ~    930 tokens
 ```
 
-### Key Benefits
-
-| Benefit | Impact | Typical Savings |
-| :--- | :--- | :--- |
-| **Surgical chunking** | AST-precise: entire functions, never split mid-logic | 84–90% token reduction |
-| **Hybrid search** | TF-IDF + semantic vectors (Ollama) rank results intelligently | +0.04 MRR, better relevance |
-| **Zero infrastructure** | Pure in-memory index, no external databases | Instant startup, zero DevOps |
-| **Air-gapped** | Works entirely locally or with local Ollama | 100% privacy, no API keys |
-| **Dependency awareness** | Every result includes topology (who calls this, what it imports) | Prevents broken refactors |
-| **Language support** | JavaScript, TypeScript, Python, Rust, Go, PHP, CSS, Java, Kotlin, C#, Ruby | Single tool for polyglot codebases |
-| **Fault tolerance** | Degrades gracefully to TF-IDF if Ollama offline | Always works |
+The difference compounds across a session. Agents that read files also lack topology — they can't see which other functions call the one they're modifying, so they miss side effects.
 
 ---
 
-## Test Results: 100% Recall, 96% MRR
-
-graph-indexer was evaluated on 5 production-grade open-source projects totaling **7,503 chunks** across JavaScript, TypeScript, Python, Go, and Ruby.
+## Results
 
-### Test Suite Performance
+Measured across 5 production open-source codebases (7,503 AST chunks, 70 ground-truth queries across 3 difficulty levels).
 
-| Project | Language | Chunks | Lexical Recall@5 | Hybrid Recall@5 | MRR Improvement |
-| :--- | :--- | :--- | :--- | :--- | :--- |
-| Axios v1.6.0 | JavaScript | 435 | 1.00 | 1.00 | — |
-| Express 4.18.2 | JavaScript | 389 | 1.00 | 1.00 | +0.06 |
-| NestJS v10.4.9 | TypeScript | 2,019 | 1.00 | 1.00 | **+0.14** |
-| FastAPI 0.103.0 | Python | 3,572 | 1.00 | 1.00 | +0.01 |
-| Gin v1.9.1 | Go | 1,088 | 1.00 | 1.00 | +0.01 |
-| **Mean** | — | **7,503** | **1.00** | **1.00** | **+0.04** |
+### Token savings per query
 
-**What this means:**
-- ✅ **100% of relevant code found in top 5 results** across every suite and language
-- ✅ **All queries return correct results rank-1** when using exact symbol names (`exact_tokens`)
-- ✅ **Mean reciprocal rank improves to 0.96** with semantic search enabled
-- ✅ **Hybrid mode adds +0.14 MRR** on NestJS (large polyglot TypeScript codebase)
-- ✅ **Graceful degradation:** lexical-only mode still achieves 1.00 recall@5 for exact-name queries
+| Project | Language | Without (full files) | With graph-indexer | Savings | Latency |
+| :--- | :--- | ---: | ---: | ---: | ---: |
+| Axios v1.6.0 | JavaScript | ~2,290 tok | ~655 tok | **71.4%** | 0.2 ms |
+| Express 4.18.2 | JavaScript | ~7,330 tok | ~850 tok | **88.4%** | 0.2 ms |
+| NestJS v10.4.9 | TypeScript | ~2,535 tok | ~900 tok | **64.5%** | 0.7 ms |
+| FastAPI 0.103.0 | Python | ~4,030 tok | ~685 tok | **83.0%** | 1.0 ms |
+| Gin v1.9.1 | Go | ~2,530 tok | ~450 tok | **82.2%** | 0.4 ms |
+| **Mean** | | | | **77.9%** | **0.5 ms** |
 
-### Query Breakdown
+> "Full files" = tokens in the source files containing the top-5 results. "With graph-indexer" = tokens in the returned chunk snippets only. Measured at 4 chars/token. NestJS is 700k tokens of source — larger than most LLMs' context windows.
 
-14–15 ground-truth queries per suite covering:
-- **Easy (3–5):** Direct function/class names (`HTTPException`, `Router`, `RequestValidator`)
-- **Medium (5–7):** Multi-token natural language (`"response send body"`, `"validate request body"`)
-- **Hard (4):** Semantic concepts with vocabulary mismatch (`"dependency injection container"`, `"content negotiation"`)
+### Search quality
 
-**Result:** Even the hardest semantic queries achieve 100% recall@5 when hybrid search is enabled.
+| Project | Chunks | Recall@1 | Recall@3 | Recall@5 | MRR |
+| :--- | ---: | ---: | ---: | ---: | ---: |
+| Axios v1.6.0 | 435 | 0.86 | 1.00 | **1.00** | 0.92 |
+| Express 4.18.2 | 389 | 0.93 | 0.93 | **1.00** | 0.95 |
+| NestJS v10.4.9 | 2,019 | 1.00 | 1.00 | **1.00** | **1.00** |
+| FastAPI 0.103.0 | 3,572 | 0.93 | 1.00 | **1.00** | 0.96 |
+| Gin v1.9.1 | 1,088 | 0.85 | 1.00 | **1.00** | 0.92 |
+| **Mean** | **7,503** | **0.91** | **0.99** | **1.00** | **0.95** |
 
-### Token Savings
-
-Average **74.6% token reduction** across all queries when using graph-indexer vs full-file reads:
-
-```
-Query: "Find the JWT validation logic"
-File-based approach:  src/auth.ts (850 lines) → 10,625 tokens
-graph-indexer:       validateToken chunk (35 lines) → 437 tokens
-                     Savings: 95.9% on this query
-```
+**Recall@5 = 1.00** across every project: the correct answer is always in the top 5. **MRR = 0.95**: the correct answer is rank 1 or 2 on average.
 
 ---
 
-## Why graph-indexer Beats Alternatives
-
-### vs. Standard RAG (ChromaDB, Pinecone, Weaviate)
-
-| Feature | **graph-indexer** | Standard RAG |
-| :--- | :--- | :--- |
-| **Infrastructure** | Zero-DB, pure in-memory `Map` | Requires external vector database |
-| **Privacy** | 100% local + air-gapped | Often sends to cloud APIs |
-| **Chunking strategy** | AST-precise (entire functions) | Naive token-count splits — breaks logic in half |
-| **Hybrid search** | TF-IDF ⊕ vectors w/ RRF fusion | Dense-only or BM25-only |
-| **Code structure** | Bidirectional dependency graph | No topology awareness |
-| **Startup time** | <100ms (memory-map index) | 5–30s (load from DB) |
-| **Cost** | $0 (local) or $5–50/month (Ollama CPU) | $0–500/month per million queries |
-| **Language support** | 11 languages with AST precision | Language-agnostic (no structure) |
+## Getting started
 
-### vs. File-Based Search (git grep, ripgrep)
-
-graph-indexer is semantic + structural, not just text matching:
-
-| Query | ripgrep | graph-indexer |
-| :--- | :--- | :--- |
-| `grep -r "ValidationError"` | Returns every line mentioning `ValidationError` (thousands of results) | Returns the definition + all places it's raised, ranked by relevance |
-| `grep -r "async function"` | Every async function in the codebase | Only async functions matching semantic context of your query |
-| Refactor safety | No way to know if rename is safe | Call graph shows every place the symbol is used |
-
----
-
----
-
-## Quick Start
+**Requirements:** Node.js v18+ · Ollama (optional, for semantic search)
 
 ### 1. Install
 
@@ -147,918 +100,330 @@ npm install graph-indexer --save-dev
 npx graph-indexer init
 ```
 
-**What `init` does:**
-- Auto-detects your IDEs (Cursor, VS Code, Claude Desktop)
-- Adds `mcp:index`, `mcp:watch`, `mcp:start` scripts to `package.json`
-- Updates `.gitignore` to exclude index files
-- Creates `.vscode/` or `.cursor/` configuration (if needed)
-
-### 2. Index Your Repository
+`init` auto-detects your IDE (Claude, Cursor, VS Code), adds npm scripts to `package.json`, updates `.gitignore`, and opens an interactive language selector:
 
-```bash
-npm run mcp:index
 ```
+⚙️  Select languages (Arrows/Tab: move, Space: toggle, Enter: confirm):
 
-**For semantic search with Ollama:**
-```bash
-# Install Ollama first: https://ollama.ai
-ollama pull nomic-embed-text
+  ❯ ◯ TypeScript / TSX         .ts, .tsx
+    ◯ JavaScript               .js, .jsx, .mjs, .cjs
+    ◯ Python                   .py
+    ◯ Go                       .go
+    ◯ Rust                     .rs
+    ◯ PHP                      .php
+    ◯ Java                     .java
+    ◯ Kotlin                   .kt, .kts
+    ◯ C#                       .cs
+    ◯ Ruby                     .rb
+    ◯ CSS / SCSS               .css, .scss
+```
 
-# Index with vectors
-npm run mcp:index  # auto-detects Ollama at http://localhost:11434
+Navigate with **↑ ↓**, toggle with **Space**, confirm with **Enter**. Leaving all unselected enables every language. Your selection is saved to `.graph-indexer.json`. Pass `--all-languages` to skip the prompt.
 
-# Or specify a different port
-OLLAMA_HOST=http://localhost:11435 npm run mcp:index
-```
+### 2. Index your codebase
 
-**For lexical-only (no Ollama):**
+**With semantic search (recommended):**
 ```bash
-INDEXER_EMBEDDINGS=off npm run mcp:index
+# Install Ollama: https://ollama.ai
+ollama pull nomic-embed-text
+npm run mcp:index
 ```
 
-### 3. Start the MCP Server
-
+**Lexical-only (no Ollama required):**
 ```bash
-npm run mcp:start
+INDEXER_EMBEDDINGS=off npm run mcp:index
 ```
 
-The server will:
-- Load the index into memory
-- Start the file watcher daemon (auto-updates on file changes)
-- Listen for MCP stdio connections
+Lexical-only still achieves Recall@5 = 1.00 on all benchmarks above.
 
-### 4. Configure Your IDE
+### 3. Configure your IDE
 
-#### **Claude Desktop** (`~/Library/Application Support/Claude/claude_desktop_config.json`)
+`init` writes the config automatically. Manual examples:
 
+**Claude Desktop** (`~/Library/Application Support/Claude/claude_desktop_config.json`):
 ```json
 {
   "mcpServers": {
     "graph-indexer": {
-      "command": "node",
-      "args": ["/path/to/your/project/node_modules/graph-indexer/mcp-server.mjs"],
-      "env": {
-        "MCP_PROJECT_ROOT": "/path/to/your/project",
-        "OLLAMA_HOST": "http://localhost:11434"
-      }
+      "command": "npm",
+      "args": ["run", "--prefix", "/path/to/project", "mcp:start"],
+      "env": { "MCP_PROJECT_ROOT": "/path/to/project" }
     }
   }
 }
 ```
 
-#### **Cursor** (`.cursor/mcp.json`)
-
+**Cursor** (`.cursor/mcp.json`) and **Claude Code** (`.mcp.json`):
 ```json
 {
   "mcpServers": {
     "graph-indexer": {
-      "command": "node",
-      "args": ["${workspaceFolder}/node_modules/graph-indexer/mcp-server.mjs"],
+      "command": "npm",
+      "args": ["run", "mcp:start"],
       "env": { "MCP_PROJECT_ROOT": "${workspaceFolder}" }
     }
   }
 }
 ```
 
-#### **VS Code** (`.vscode/mcp.json`)
-
+**VS Code** (`.vscode/mcp.json`):
 ```json
 {
   "servers": {
     "graph-indexer": {
       "type": "stdio",
-      "command": "node",
-      "args": ["${workspaceFolder}/node_modules/graph-indexer/mcp-server.mjs"]
+      "command": "npm",
+      "args": ["run", "mcp:start"],
+      "env": { "MCP_PROJECT_ROOT": "${workspaceFolder}" }
     }
   }
 }
 ```
 
----
-
-## How It Works
-
-```mermaid
-flowchart LR
-    INPUT["Source Files\n(.ts .js .py .rs .go .php .css)"]
-    PARSE["Tree-sitter\nAST Parser"]
-    CHUNKS["Semantic Chunk\nExtractor\n(functions • classes • impls)"]
-    DEPS["Bidirectional\nImport Map"]
-    
-    TFIDF["TF-IDF Inverted\nIndex"]
-    EMBED["Ollama\nnomic-embed-text"]
-    VECTORS["Float32Array\nVector Matrix"]
-    
-    GRAPH["Dependency\nGraph"]
-    
-    FUSION["RRF Fusion\nLexical + Vector"]
-    BOOST["Exact-Name\nBoost"]
-    
-    TOOLS["MCP Tools"]
-    SEARCH["search_code"]
-    CHUNK_GET["get_chunk"]
-    SKELETON["get_file_skeleton"]
-    CALLGRAPH["get_call_graph"]
-
-    INPUT --> PARSE --> CHUNKS --> TFIDF & DEPS
-    CHUNKS --> EMBED --> VECTORS
-    TFIDF --> FUSION
-    VECTORS --> FUSION
-    DEPS --> GRAPH
-    FUSION --> BOOST --> TOOLS
-    TOOLS --> SEARCH & CHUNK_GET & SKELETON & CALLGRAPH
-    GRAPH --> TOOLS
-```
-
-### Three-Step Process
-
-1. **Parse** (~50–100 ms per 10k files)
-   - Tree-sitter builds AST for each file
-   - Extract all named chunks (functions, classes, methods, exports)
-   - Build bidirectional import dependency map
+### 4. Add the agent system prompt
 
-2. **Index** (~2 mins for a 3,600-chunk corpus)
-   - Compute TF-IDF inverted index (lexical search)
-   - Call Ollama to generate `nomic-embed-text` vectors (~384–768 dimensions)
-   - Build `Float32Array` dense matrix for cosine similarity search
-   - Serialize both to disk-efficient JSON + binary formats
-
-3. **Search**
-   - Query arrives: "Find the token validation function"
-   - Lexical search via TF-IDF (instant)
-   - Vector search via `Float32Array` cosine (1–5 ms for 1k–10k chunks)
-   - Merge results using Reciprocal Rank Fusion (RRF) with K=60
-   - Apply exact-name boost if `exact_tokens` provided
-   - Return top-k results with topology (calls, imports, imported-by)
-
----
+Copy [PROMPT.md](./PROMPT.md) into your AI agent's system prompt to instruct it to use graph-indexer tools instead of reading files directly.
 
 ---
 
-## System Requirements
-
-| Requirement | Details |
-| :--- | :--- |
-| **Node.js** | v18+ (ES Modules) |
-| **Ollama** | Optional. Runs locally for embedding generation. Pull `nomic-embed-text` to enable semantic search. |
-| **Disk** | `code-index.json` (metadata) + `code-index.embeddings.bin` (binary float32 vectors). Both are gitignored by default. |
-
-### Ollama Setup (Optional but Recommended)
-
-```bash
-# Install Ollama: https://ollama.ai
-ollama pull nomic-embed-text
-npm run mcp:index   # now with semantic vectors
-```
-
-### Lexical-Only Mode (No Ollama Required)
-
-```bash
-INDEXER_EMBEDDINGS=off npm run mcp:index
-```
-
-Recall@3 remains 100% for exact-name queries. Semantic recall (concept-to-code) degrades to lexical-only; still effective for most programming tasks.
+## MCP tools
 
-### Custom Ollama Host
+### `search_code`
 
-```bash
-# Non-standard port
-OLLAMA_HOST=http://localhost:11435 npm run mcp:index
+Hybrid BM25 + vector search over the index. The primary entry point for agents.
 
-# Remote server
-OLLAMA_HOST=http://192.168.1.100:11434 npm run mcp:index
-```
+| Parameter | Type | Default | Description |
+| :--- | :--- | :--- | :--- |
+| `query` | string | required | Natural language description of the logic to find |
+| `exact_tokens` | string? | — | Exact symbol name — guarantees rank-1 placement |
+| `detail` | `"signatures"` \| `"smart"` \| `"full"` | `"smart"` | How much code to return per result |
+| `top_k` | number | `5` | Results to return (1–20) |
+| `include_topology` | boolean | `true` | Include imports / used-by / calls |
+| `min_score` | number | `0.3` | Minimum relevance threshold |
+| `token_budget` | number? | auto | Cap total tokens returned |
+
+**`detail` levels:**
+
+| Value | Cost | Returns |
+| :--- | ---: | :--- |
+| `"signatures"` | ~20 tok | Name, type, params, return type, topology |
+| `"smart"` (default) | ~150 tok | Signature + lines relevant to the query |
+| `"full"` | ~300 tok | Signature + complete source body |
 
 ---
 
-## MCP Tools Reference
+### `resolve_symbol`
 
-### `search_code`
+O(1) lookup by exact name — no search ranking needed.
 
-Hybrid semantic + lexical search. Returns compact signature cards for all results, then fills remaining token budget with code bodies.
-
-| Parameter | Type | Default | Description |
-| :--- | :--- | :--- | :--- |
-| `query` | `string` | — | Natural language description of the logic to find |
-| `exact_tokens` | `string?` | — | Exact symbol name to guarantee rank-1 placement |
-| `top_k` | `number` | `5` | Number of results (1–20) |
-| `min_score` | `number` | `0.3` | Minimum cosine similarity threshold |
-| `token_budget` | `number?` | 1500 chars | Estimated token budget for code bodies |
-| `include_topology` | `boolean` | `true` | Include `⬇️ Deps` / `⬆️ Used by` / `🔗 Calls` in output |
-
-**Example response:**
-```
-#1 · validateToken [function_declaration]
-📄 src/utils/jwt.ts:14–42 · ID: `a3f9c1b2` · RRF: 0.0321
-💬 Validates and decodes a JWT access token. Throws on expiry.
-⬇️  Deps:    src/config/env.ts [JWT_SECRET] | src/utils/errors.ts [AuthError]
-⬆️  Used by: src/middleware/auth.ts, src/routes/api.ts
-🔗 Calls:   verify, decodePayload, throwIfExpired
-↩️  Expand body: get_chunk("a3f9c1b2")
-```
+| Parameter | Type | Description |
+| :--- | :--- | :--- |
+| `symbol` | string | Exact function, class, or type name (e.g. `"validateToken"`) |
 
 ---
 
-## MCP Tools Reference
+### `get_chunk`
 
-### `search_code(query, exact_tokens?, top_k?, min_score?, token_budget?, include_topology?)`
-
-Hybrid semantic + lexical search. Returns ranked chunks with their signatures, dependencies, and call graph. Token budget is distributed across all results.
+Returns the source code of a single chunk by its ID.
 
 | Parameter | Type | Default | Description |
 | :--- | :--- | :--- | :--- |
-| `query` | string | (required) | Natural language or descriptive phrase (e.g., "JWT validation") |
-| `exact_tokens` | string | — | Exact symbol name for guaranteed rank-1 placement (e.g., "validateToken") |
-| `top_k` | number | 5 | Results to return (1–20) |
-| `min_score` | number | 0.3 | Minimum RRF score threshold (0.0–1.0) |
-| `token_budget` | number | 4000 | Max tokens to spend on code bodies |
-| `include_topology` | boolean | true | Include dependencies + call graph in results |
-
-**Search Strategy:**
-1. Query is embedded via Ollama (or skipped in lexical-only mode)
-2. Parallel search: TF-IDF + vector similarity
-3. Results merged using Reciprocal Rank Fusion (K=60) with weighted fusion
-4. Exact-name token boost applied if provided
-5. Results ranked by combined score
-
-**Example Usage:**
-```
-search_code(
-  query="JWT payload validation and expiry check",
-  exact_tokens="validateToken",
-  top_k=3,
-  include_topology=true
-)
-```
+| `chunk_id` | string | required | ID from `search_code` results |
+| `view` | `"full"` \| `"signature"` | `"full"` | Full body or first line only |
 
-**Example Response:**
-```
-#1 · validateToken [function_declaration]
-📄 src/auth/jwt.ts:18–42 · ID: a3f9c1b2 · Score: 0.98
-💬 Validates and decodes JWT token, checks expiry timestamp
-⬇️  Dependencies: src/config/constants.ts [JWT_SECRET], src/utils/errors.ts [TokenExpiredError]
-⬆️  Used by: src/middleware/authMiddleware.ts, src/routes/protected.ts
-🔗 Calls: verify(token), parseJWT(decoded), throwIfExpired(exp)
-ℹ️  Expand: get_chunk("a3f9c1b2")
-
-#2 · parseTokenClaims [function_declaration]
-📄 src/auth/jwt.ts:45–60 · ID: c2b5d4e1 · Score: 0.82
-...
-```
+---
 
-### `get_chunk(chunk_id)`
+### `get_chunk_summary`
 
-Retrieves the full source code of one chunk by its ID (shown in search results).
+Signature + docstring + calls without the body. ~50 tokens vs ~300 for full.
 
 | Parameter | Type | Description |
 | :--- | :--- | :--- |
-| `chunk_id` | string | The ID from `search_code` results |
+| `chunk_id` | string | ID from `search_code` results |
 
-**Use when:** You need the complete body of a function/class found by search (much cheaper than reading the full file).
+---
 
-### `get_file_skeleton(file_path)`
+### `get_file_skeleton`
 
-Returns all top-level exports and definitions in a file with line numbers — no code bodies.
+All top-level exports and definitions in a file with line numbers — no bodies.
 
 | Parameter | Type | Description |
 | :--- | :--- | :--- |
-| `file_path` | string | Relative path (e.g., `src/utils/auth.ts`) |
+| `file_path` | string | Relative path (e.g. `src/utils/auth.ts`) |
 
-**Example Response:**
-```
-Exports in src/utils/auth.ts:
-  • validateToken (function) — lines 12–38
-  • hashPassword (function) — lines 40–55
-  • comparePassword (function) — lines 57–68
-  • AuthError (class) — lines 70–90
-```
-
-**Use when:** You need to understand what a file exports without reading it all (~50 tokens vs 5000).
+---
 
-### `get_call_graph(target_function)`
+### `get_call_graph`
 
-Finds all chunks that call a specific function by name.
+Every chunk across the repo that calls a specific function.
 
 | Parameter | Type | Description |
 | :--- | :--- | :--- |
-| `target_function` | string | Exact function name (e.g., `validateToken`) |
-
-**Example Response:**
-```
-Calls to validateToken:
-  • src/middleware/authMiddleware.ts:32 — in middleware function
-  • src/routes/api.ts:128 — in route handler
-  • src/services/auth.ts:44 — in login service
-```
+| `target_function` | string | Exact function name (e.g. `"validateToken"`) |
 
-**Use when:** Before renaming or modifying a function, know all dependent call sites.
-
-### `graph://dependencies/{file_path}` (Resource)
-
-Fetches the complete import/export topology for a file without search quota.
-
-**Example:**
-```
-graph://dependencies/src/middleware/auth.ts
-```
-
-**Returns:**
-```
-Imports:
-  src/config/constants.ts [JWT_SECRET]
-  src/utils/errors.ts [TokenExpiredError]
-  src/types/auth.ts [AuthRequest]
-
-Imported by:
-  src/app.ts
-  src/routes/protected.ts
-```
+Call this before modifying any exported function to find all affected call sites.
 
 ---
 
-## Hybrid RRF Search Algorithm
-
-The core innovation of graph-indexer is combining dense semantic vectors with sparse lexical signals using Reciprocal Rank Fusion:
-
-### Lexical Search: TF-IDF
-
-Each token is scored using **sublinear term frequency**:
-
-$$w(t, d) = (1 + \log \text{count}(t, d)) \times \log \frac{N}{n_t}$$
-
-Where:
-- `count(t, d)` = occurrences of term t in chunk d
-- `N` = total chunks
-- `n_t` = chunks containing term t
-
-This prevents common keywords (`return`, `const`, `if`) from dominating results.
-
-### Vector Search: Cosine Similarity
-
-Query and chunks are embedded via Ollama `nomic-embed-text` (384–768 dimensions):
-
-$$\text{sim}(q, d) = \frac{\mathbf{e}_q \cdot \mathbf{e}_d}{|\mathbf{e}_q| \times |\mathbf{e}_d|}$$
-
-Stored as pre-normalized `Float32Array` for sub-millisecond cosine computation.
-
-### Reciprocal Rank Fusion (RRF) with Weighting
-
-Results from both methods are merged using weighted RRF:
-
-$$\text{score}(d) = w_\text{lex} \cdot \frac{1}{K + r_\text{lex}(d)} + w_\text{vec} \cdot \frac{1}{K + r_\text{vec}(d)}$$
-
-**Default weights:**
-- `w_lex` = 1.5 (lexical: prioritizes exact terms)
-- `w_vec` = 1.0 (semantic: provides context)
-- `K` = 60 (rank discount constant)
-
-**Why this works:**
-- Prevents vector results from overwhelming precise lexical matches
-- Ensures "exact" queries stay exact while allowing semantic queries
-- Tested on 5 production projects: +0.04 mean MRR improvement (0.92 → 0.96)
-
-### Exact-Name Boost
-
-If `exact_tokens` parameter is provided, any chunk whose name exactly matches receives a boost:
-
-$$\text{score}_\text{final}(d) = \text{score}(d) + \frac{1}{K+1}$$
-
-This guarantees rank-1 placement for exact symbol name queries.
-
-### Demotion Strategies
-
-The following chunks receive reduced scoring:
+### `get_repo_map`
 
-- **Test/spec files** (paths matching `/test|spec|\.test\.|\.spec\.`): 0.25× multiplier
-- **Example/tutorial dirs** (paths matching `/example|doc|tutorial`): 0.5× multiplier
-- **Expression statements** (standalone expressions, not declarations): 0.8× multiplier
+Compact symbol map ordered by PageRank (most-imported files first). Orients agents in an unfamiliar codebase in ~1,500 tokens.
 
-This prevents test code from shadowing production code.
-
----
-
-## Supported Languages
-
-| Language | Extensions | Chunk Types | Import Resolution |
+| Parameter | Type | Default | Description |
 | :--- | :--- | :--- | :--- |
-| TypeScript / TSX | `.ts`, `.tsx` | functions, classes, methods, exports | Absolute & relative paths |
-| JavaScript | `.js`, `.jsx`, `.mjs`, `.cjs` | functions, classes, expressions | Absolute & relative paths |
-| Python | `.py` | function_definition, class_definition | Relative imports (`.`, `..`) → file paths |
-| Rust | `.rs` | fn, struct, enum, trait, impl | `crate::` path resolution |
-| Go | `.go` | function_declaration, method, type | Import spec resolution |
-| PHP | `.php` | function, class | include/require paths |
-| CSS / SCSS | `.css`, `.scss` | rule_set | — |
-| Java | `.java` | class, method, interface, constructor, enum | `import_declaration` → package path |
-| Kotlin | `.kt`, `.kts` | function, class, object, companion, constructor | `import_header` → package path |
-| C# | `.cs` | class, method, interface, constructor, enum, property | `using_directive` → namespace |
-| Ruby | `.rb` | method, singleton_method, class, module | `require` / `require_relative` → file path |
+| `path_filter` | string? | — | Limit to files whose path contains this string |
+| `max_files` | number | `80` | Maximum files to include |
+| `sort_by` | `"importance"` \| `"path"` | `"importance"` | Sort order |
 
 ---
 
-## Performance Characteristics
-
-### Query Latency
-
-| Corpus Size | Lexical Search | Vector Search | RRF Merge |
-| :--- | :--- | :--- | :--- |
-| 1,000 chunks | <0.5 ms | 0.8 ms | <0.1 ms |
-| 5,000 chunks | <0.8 ms | 3.2 ms | <0.1 ms |
-| 10,000 chunks | <1.2 ms | 8.5 ms | <0.2 ms |
-| 20,000+ chunks | <2 ms | 20–50 ms | <0.3 ms |
+### `list_index_stats`
 
-*Measured on V8 with pre-normalized vectors. Latency includes index lookup but not Ollama network RTT.*
-
-### Memory Footprint
-
-- **TF-IDF index:** ~150–200 bytes per chunk
-- **Vector matrix:** ~3,072 bytes per chunk at 768 dimensions (4 bytes × 768 floats)
-- **Metadata:** ~200–500 bytes per chunk (path, name, docstring refs)
-
-**Example:** A 3,600-chunk corpus occupies ~12–15 MB in memory.
-
-### Token Savings
-
-Average across 5 test suites: **74.6%** token reduction vs full-file reads.
-
-```
-Example: Express.js QuerySearch
-File read:  src/router.js (460 lines) = 5,750 tokens
-Indexed:    findRoute (65 lines)     = 812 tokens
-Savings:    86% reduction
-```
-
-### Accuracy Over Scale
-
-| Project | Total Chunks | Recall@5 | Mean MRR | Queries |
-| :--- | :--- | :--- | :--- | :--- |
-| Axios | 435 | 1.00 | 0.96 | 12 |
-| Express | 389 | 1.00 | 1.00 | 14 |
-| NestJS | 2,019 | 1.00 | 1.00 | 15 |
-| FastAPI | 3,572 | 1.00 | 0.93 | 13 |
-| Gin | 1,088 | 1.00 | 0.92 | 11 |
-| **Mean** | **7,503** | **1.00** | **0.96** | **65** |
-
-- **Recall@5:** 100% of relevant chunks found in top 5 results
-- **Mean MRR:** Average reciprocal rank of first correct result
-- **Query types:** Easy (exact symbol), Medium (multi-token), Hard (semantic mismatch)
+Index health snapshot: chunk count, file count, symbol table size, vector count, search mode, daemon status, index age.
 
 ---
 
-### Vector Search Performance
+### `graph://dependencies/{file_path}` (resource)
 
-| Corpus size | Pure JS flat scan | HNSW (auto-activated ≥5k) |
-| :--- | :--- | :--- |
-| 1,000 chunks (dim=768) | 0.9 ms/query | — |
-| 5,000 chunks (dim=768) | 4.5 ms/query | 1.2 ms/query |
-| 20,000 chunks (dim=768) | 30.5 ms/query | 3.1 ms/query |
+Full bidirectional dependency topology for a file: what it imports and what imports it.
 
 ---
 
-## Best Practices for Maximum Recall
-
-### 1. Write Comprehensive JSDoc/TSDoc
-
-The indexer embeds your docstrings alongside code bodies. Better docstrings = better semantic search:
-
-```typescript
-/**
- * Validates and decodes a JWT access token.
- * 
- * Checks token signature, expiry timestamp, and claims payload.
- * Throws if token is malformed, expired, or signed with wrong key.
- *
- * @param token - Raw JWT string from Authorization header
- * @param options - Optional validation parameters
- * @returns Decoded token payload with user ID, role, and expiry time
- * @throws AuthError if validation fails
- * 
- * @example
- * const payload = validateToken(req.headers.authorization);
- * console.log(payload.userId, payload.role);
- */
-export function validateToken(token: string, options?: ValidationOptions): TokenPayload { ... }
-```
-
-### 2. Use Descriptive, Specific Names
-
-The exact-name boost ranks any chunk whose name matches `exact_tokens` at position #1. Specific names unlock this:
-
-```typescript
-// ✅ Exact-name searchable
-export const useNotificationPermissionStatus = () => { ... };
-export function calculateTripDurationInDays(start: Date, end: Date) { ... };
-export async function fetchAndCacheUserProfile(userId: string) { ... }
-
-// ❌ Generic — impossible to target without semantic search
-export const util = () => { ... };
-export function process(data: any) { ... }
-export async function fetch(path: string) { ... }
-```
-
-### 3. Export Named Helpers, Not Anonymous Functions
-
-Named exports become searchable chunks:
-
-```typescript
-// ✅ Indexed as chunk
-export function validatePaymentMethod(card: Card): boolean {
-  // validation logic
-}
+## Configuration
 
-// ❌ Not indexed (anonymous)
-const validate = (card: Card) => { ... };
-export default validate;
-```
+### Environment variables
 
-### 4. Add Docstrings to Class Methods
+| Variable | Default | Description |
+| :--- | :--- | :--- |
+| `MCP_PROJECT_ROOT` | `process.cwd()` | Project root directory |
+| `OLLAMA_HOST` | `http://localhost:11434` | Ollama API endpoint |
+| `INDEXER_EMBEDDINGS` | — | Set to `off` to disable vector embeddings |
 
-Even small methods benefit from docstrings:
+### Language selection
 
-```typescript
-class PaymentService {
-  /**
-   * Charges customer card via Stripe API.
-   * Throws on declined card or network failure.
-   */
-  async chargeCard(cardToken: string, amount: number): Promise<Charge> {
-    // ...
-  }
+`init` saves your selection to `.graph-indexer.json` in the project root:
 
-  /**
-   * Refunds transaction to original payment method.
-   */
-  async refundCharge(chargeId: string): Promise<Refund> {
-    // ...
-  }
-}
+```json
+{ "languages": ["typescript", "javascript", "python"] }
 ```
 
-### 5. Minimize Generic Utility Files
-
-Files with <5 indexable chunks produce weak search signals:
-
-```typescript
-// ❌ Won't index well (2 lines)
-export const AuthContext = createContext(null);
-export const useAuth = () => useContext(AuthContext);
-
-// ✅ Indexable
-/**
- * Context for accessing authentication state throughout component tree.
- * Provides currentUser, isLoading, error from nearest AuthProvider.
- */
-export const AuthContext = createContext<AuthContextValue | null>(null);
-
-/**
- * Hook to access authentication state.
- * Throws if used outside AuthProvider.
- * @returns Authenticated user, loading state, and any auth errors
- */
-export function useAuth(): AuthContextValue {
-  const ctx = useContext(AuthContext);
-  if (!ctx) throw new Error('useAuth must be called inside <AuthProvider>');
-  return ctx;
-}
-```
+Valid keys: `typescript`, `javascript`, `python`, `go`, `rust`, `php`, `java`, `kotlin`, `csharp`, `ruby`, `css`.
 
----
+Update at any time by re-running `init`:
 
-## Architecture & Implementation
-
-### File Structure
-
-```
-graph-indexer/
-├── core-engine.mjs              # In-memory dual index: TF-IDF + vector matrix
-│                                 # Methods: search(), searchHybrid(), save(), load()
-├── parser-utils.mjs             # Tree-sitter AST parsing + Ollama embedding
-│                                 # Supports 11 languages with AST-precision chunking
-├── indexer.mjs                  # CLI entry: scans repo → parses → embeds → saves
-├── watch-daemon.mjs             # Chokidar file watcher for incremental index updates
-├── mcp-server.mjs               # MCP stdio server: exposes search_code, get_chunk, etc.
-├── init.mjs                     # Installation & IDE configuration helper
-├── PROMPT.md                    # Agent system prompt for AI coding agents
-├── tests/
-│   ├── harness.mjs              # Shared test execution framework
-│   ├── run.mjs                  # Lexical-only evaluation harness
-│   ├── run-embeddings.mjs       # Hybrid (Ollama) evaluation harness
-│   ├── metrics.mjs              # Recall, MRR, latency calculations
-│   ├── suites/
-│   │   ├── axios.mjs            # 435-chunk corpus, 12 queries
-│   │   ├── express-js.mjs       # 389-chunk corpus, 14 queries
-│   │   ├── fastapi.mjs          # 3,572-chunk corpus, 13 queries
-│   │   ├── gin.mjs              # 1,088-chunk corpus, 11 queries
-│   │   └── nestjs.mjs           # 2,019-chunk corpus, 15 queries
-│   ├── reports/                 # JSON performance reports
-│   └── ...
-├── package.json
-├── README.md
-└── LICENSE
+```bash
+npx graph-indexer init                    # Re-run interactive selector
+npx graph-indexer init --all-languages   # Enable all, no prompt
 ```
 
-### Indexing Pipeline
-
-1. **Discovery** (15–50 ms)
-   - Recursively scan directory
-   - Apply `.gitignore` filters (vendor, node_modules)
-   - Collect source file paths
-
-2. **Parsing** (50–500 ms)
-   - Tree-sitter parses each file
-   - Extract semantic chunks: functions, classes, methods, exports
-   - Build bidirectional import dependency graph
-
-3. **Embedding** (1–10 mins for 5k chunks)
-   - Batch chunks into 32-chunk requests
-   - Call Ollama `/api/embed` with "search_document:" prefix
-   - Store vectors as `Float32Array` binary matrix
-
-4. **Indexing** (20–50 ms)
-   - Build TF-IDF inverted index (token → chunk IDs)
-   - Compute IDF for each term
-   - Build dependency graph adjacency maps
-
-5. **Serialization** (100–300 ms)
-   - Save metadata to `code-index.json`
-   - Write vectors to `code-index.embeddings.bin` (binary float32)
-   - Atomic `tmp → rename` for crash safety
+If `.graph-indexer.json` is absent or has no `languages` key, all installed parsers are used.
 
 ---
 
-## Configuration & Tuning
-
-### Environment Variables
+## Supported languages
 
-| Variable | Default | Description |
+| Language | Extensions | Chunks extracted |
 | :--- | :--- | :--- |
-| `OLLAMA_HOST` | `http://localhost:11434` | Ollama API endpoint |
-| `INDEXER_EMBEDDINGS` | — | Set to `off` to disable embeddings (lexical-only mode) |
-| `MCP_PROJECT_ROOT` | `process.cwd()` | Project root path for relative import resolution |
-| `INDEXER_LOG_LEVEL` | `info` | Logging verbosity: `debug`, `info`, `warn`, `error` |
-
-### Advanced Tuning
-
-Edit `core-engine.mjs` to adjust these constants:
-
-```javascript
-// Weighted RRF parameters
-const RRF_K = 60;              // Discount constant
-const LEX_WEIGHT = 1.5;        // Lexical weight (1.0–2.0)
-const VEC_WEIGHT = 1.0;        // Vector weight (0.5–1.5)
-
-// Demotion multipliers
-const TEST_FILE_DEMOTION = 0.25;      // Test files: 0.25× score
-const EXAMPLE_DIR_DEMOTION = 0.5;     // Example dirs: 0.5× score
-const EXPRESSION_DEMOTION = 0.8;      // Standalone expressions: 0.8× score
-
-// Name boost
-const EXACT_NAME_TOKEN_BOOST = 1.4;   // Boost for exact token matches
-```
-
-**Guidelines:**
-- Increase `LEX_WEIGHT` if exact-symbol queries underperform
-- Increase `VEC_WEIGHT` if semantic queries need more influence
-- Lower `TEST_FILE_DEMOTION` if tests contain important reference code
+| TypeScript / TSX | `.ts`, `.tsx` | functions, classes, methods, exports |
+| JavaScript | `.js`, `.jsx`, `.mjs`, `.cjs` | functions, classes, expressions |
+| Python | `.py` | functions, classes |
+| Go | `.go` | functions, methods, types |
+| Rust | `.rs` | fn, struct, enum, trait, impl |
+| Java | `.java` | class, method, interface, constructor, enum |
+| Kotlin | `.kt`, `.kts` | function, class, object, companion |
+| C# | `.cs` | class, method, interface, property, enum |
+| Ruby | `.rb` | method, class, module |
+| PHP | `.php` | function, class |
+| CSS / SCSS | `.css`, `.scss` | rule sets |
 
 ---
 
-## Troubleshooting
-
-### Q: Index takes forever to build
-**Symptom:** `npm run mcp:index` hangs on "Embedding chunks..."
+## How it works
 
-**Solutions:**
-1. Verify Ollama is running: `curl http://localhost:11434/api/tags`
-2. Check your internet/network (Ollama might be on remote host)
-3. Use lexical-only mode: `INDEXER_EMBEDDINGS=off npm run mcp:index`
-4. Monitor Ollama memory: large corpora may need 4–8GB
+### Indexing
 
-### Q: Search results are irrelevant
-**Symptom:** Queries return wrong chunks even though correct chunk exists
+When you run `npm run mcp:index`:
 
-**Solutions:**
-1. Check if chunk is indexed: `grep "chunk_name" code-index.json`
-2. If missing, ensure chunk has a descriptive name (see Best Practices)
-3. Try with `exact_tokens`: `search_code(query, exact_tokens="chunk_name")`
-4. Increase `top_k` to see more candidates
-5. Verify Ollama model is loaded: `ollama list` should show `nomic-embed-text`
+1. **Parses** every source file with Tree-sitter — no regex, exact AST boundaries.
+2. **Extracts chunks**: named functions, classes, methods, and exports, each with name, docstring, parameters, return type, call sites, and type references.
+3. **Builds a dependency graph**: bidirectional import map so each chunk knows what it imports and what imports it.
+4. **Creates two indexes**: a BM25 inverted index (lexical) and per-chunk float32 embeddings via Ollama `nomic-embed-text` (optional).
+5. **Serializes to disk**: `code-index.json` + `code-index.embeddings.bin`.
 
-### Q: Ollama connection fails
-**Symptom:** Error: "Failed to connect to Ollama at http://localhost:11434"
+A background watcher daemon re-indexes changed files automatically.
 
-**Solutions:**
-```bash
-# 1. Verify Ollama is running
-ollama list
-
-# 2. Check port (might be on different port)
-curl http://localhost:11434/api/tags    # default
-curl http://localhost:11435/api/tags    # alternative
+### Search pipeline
 
-# 3. Specify different host
-OLLAMA_HOST=http://192.168.1.100:11434 npm run mcp:index
-
-# 4. Fallback to lexical-only
-INDEXER_EMBEDDINGS=off npm run mcp:index
+```
+Source files
+     │
+     ▼
+Tree-sitter AST
+     │
+     ├──► Chunks ──► BM25 inverted index ──┐
+     │         └──► Float32 embeddings  ──┤── RRF fusion ──► Ranked results ──► MCP tools
+     │                                     │
+     └──► Dependency graph ────────────────┘
 ```
 
-### Q: MCP server won't start
-**Symptom:** Error when connecting IDE to MCP server
-
-**Solutions:**
-1. Verify index exists: `ls -la code-index.json`
-2. Check MCP_PROJECT_ROOT: `echo $MCP_PROJECT_ROOT` should point to project
-3. Test stdio: `node mcp-server.mjs` (should wait for input)
-4. Check IDE config paths are absolute, not relative
-
-### Q: Memory usage is too high
-**Symptom:** Node process consuming 2GB+
-
-**Solutions:**
-- Large corpora (10k+ chunks) require 1–2GB
-- Use `--max-old-space-size` flag:
-  ```bash
-  node --max-old-space-size=4096 node_modules/graph-indexer/mcp-server.mjs
-  ```
-- Consider splitting into multiple projects
-- Use lexical-only mode to reduce vector matrix size by 75%
-
-### Q: Incremental updates aren't working
-**Symptom:** File changes not reflected in search results
-
-**Solutions:**
-1. Manually re-index: `npm run mcp:index`
-2. Check watcher is running: `npm run mcp:watch`
-3. Verify file changes are within project root (check `.gitignore`)
-4. Restart MCP server after index updates
+1. **BM25 lexical search** — O(query_terms) over the inverted index.
+2. **Vector search** — cosine similarity over pre-normalized float32 embeddings.
+3. **RRF fusion** merges both lists (lexical 1.5×, vector 1.0×).
+4. **Score boosts**: exact name match +2.0×, suffix match +1.4×, path token +1.4×, test files demoted.
 
 ---
 
-## FAQ
-
-### How much faster is graph-indexer vs file reads?
+## Best practices
 
-- **Token usage:** 84–90% reduction (see test results above)
-- **Latency:** 1–50 ms per query vs 500ms+ for file I/O + token counting
-- **Accuracy:** Same relevance, but 100% recall@5 with better context
+**Write descriptive docstrings.** Docstrings are embedded alongside code — better documentation directly improves semantic search quality.
 
-### Can I use it without Ollama?
+**Use specific function names.** Names like `fetchAndCacheUserProfile` trigger the exact-name boost (2.0×) and reliably appear as rank-1 results when queried by name.
 
-Yes. Run with `INDEXER_EMBEDDINGS=off npm run mcp:index`. You get:
-- Pure TF-IDF lexical search
-- Exact-name queries still work perfectly
-- Semantic queries degrade to string matching
-- 1.00 recall@5 for exact-symbol searches
+**Export named functions, not anonymous ones.** Anonymous default exports can't be targeted by `resolve_symbol` and rank lower in name-boost scoring.
 
-### Does it support monorepos?
+**Avoid catch-all utility files.** Files that mix unrelated utilities produce weaker per-chunk signals. One responsibility per module indexes more cleanly.
 
-Partially. The indexer creates one `code-index.json` per directory. For monorepos:
-1. Index each service separately
-2. Or create a wrapper that merges multiple indexes
-3. Or use a single MCP server per service
-
-### What file types are indexed?
-
-See Supported Languages table. Only recognized languages are parsed. Other files (configs, docs) are skipped.
-
-### Can I make the index portable?
-
-Yes. Both `code-index.json` and `code-index.embeddings.bin` are self-contained. Copy them to another machine and start the MCP server — it works immediately.
-
-### How does performance scale?
+---
 
-- Parsing: O(file_size_total) — linear
-- TF-IDF indexing: O(tokens × unique_terms) — sublinear with repetition
-- Vector search: O(chunks) flat scan, O(log chunks) with HNSW index
-- For 5k chunks: ~2 mins to index, 1–5ms per query
+## Troubleshooting
 
----
+**Index takes too long**
+- Verify Ollama is running: `curl http://localhost:11434/api/tags`
+- Use lexical-only mode: `INDEXER_EMBEDDINGS=off npm run mcp:index`
 
-## Index Files Reference
+**Search returns irrelevant results**
+- Use `exact_tokens` for known symbol names
+- Check coverage with `list_index_stats()`
+- Increase `top_k` to see more candidates
 
-| File | Format | Purpose | Size | Portable |
-| :--- | :--- | :--- | :--- | :--- |
-| `code-index.json` | JSON | Chunk metadata, TF-IDF inverted index, dependency graph | ~200 KB / 1k chunks | ✅ Yes |
-| `code-index.embeddings.bin` | Binary float32 | Vector embeddings (pre-normalized for cosine) | ~3 MB / 1k @768-dim | ✅ Yes |
+**MCP server won't connect**
+- Verify `MCP_PROJECT_ROOT` points to the indexed directory
+- Check `code-index.json` exists: `ls -la code-index.json`
+- Test manually: `npm run mcp:start`
 
-Both are gitignored by default. Regenerate with `npm run mcp:index` whenever you want a fresh index.
+**Results are stale after file changes**
+- The daemon auto-updates; if stale, run `npm run mcp:index` manually
+- Check daemon status with `list_index_stats()`
 
 ---
 
-## Contributing & Development
-
-### Building from Source
+## Development
 
 ```bash
 git clone https://github.com/MaquinaTech/graph-indexer.git
 cd graph-indexer
 npm install
-npm run mcp:index  # index this repo
-npm run test       # run test suite
-npm run mcp:start  # start MCP server for development
-```
-
-### Running Tests
-
-```bash
-# Test lexical-only mode
-npm run test
-
-# Test hybrid mode (requires Ollama)
-npm run test:embeddings
-
-# Generate performance report
-npm run test:report
+npm run mcp:index   # index this repo
+npm run test        # run test suite (lexical-only)
+npm run mcp:start   # start MCP server
 ```
 
-### Project Philosophy
-
-1. **Local First:** No external dependencies beyond Ollama (optional)
-2. **AST-Precise:** Tree-sitter for exact code boundaries, not fuzzy chunks
-3. **Hybrid Search:** Combine lexical + semantic for both accuracy and recall
-4. **Zero Database:** In-memory only, no infrastructure required
-5. **Production-Grade:** 100% recall on 5 production projects
-
-### Roadmap
-
-- [ ] HNSW indexing for vector search >20k chunks
-- [ ] Incremental embedding updates (batch new files only)
-- [ ] Language server protocol (LSP) integration
-- [ ] Web UI for search visualization
-- [ ] Multi-repo federation mode
-- [ ] Custom embedding model support
-
 ---
 
 ## License
 
-Released under the [MIT License](LICENSE).
-
-Copyright (c) 2026 MaquinaTech. Free to use, modify, and distribute in both open-source and commercial projects.
-
----
-
-## Author & Support
-
-Built and maintained by **MaquinaTech**.
-
-- **GitHub:** [github.com/MaquinaTech](https://github.com/MaquinaTech)
-- **NPM:** [npmjs.com/package/graph-indexer](https://www.npmjs.com/package/graph-indexer)
-- **Issues & Feedback:** [github.com/MaquinaTech/graph-indexer/issues](https://github.com/MaquinaTech/graph-indexer/issues)
-
-Issues, pull requests, and feature discussions are welcome. This project started as a solution to the context bloat problem in AI coding agents — we'd love to hear how you're using it.
-
----
-
-## Test Methodology
-
-All results in this README come from rigorous evaluation across 5 production-grade open-source projects:
-
-### Test Suites
-
-1. **Axios v1.6.0** (JavaScript HTTP client)
-   - 435 total chunks, 12 ground-truth queries
-   - Coverage: request/response handling, middleware, interceptors
-
-2. **Express.js v4.18.2** (JavaScript web framework)
-   - 389 total chunks, 14 ground-truth queries
-   - Coverage: routing, middleware, response handling
-
-3. **NestJS v10.4.9** (TypeScript framework)
-   - 2,019 total chunks, 15 ground-truth queries
-   - Coverage: decorators, dependency injection, modules, controllers
-
-4. **FastAPI v0.103.0** (Python async framework)
-   - 3,572 total chunks, 13 ground-truth queries
-   - Coverage: route handlers, dependency injection, middleware
-
-5. **Gin v1.9.1** (Go web framework)
-   - 1,088 total chunks, 11 ground-truth queries
-   - Coverage: routing, middleware, context handling
-
-### Evaluation Metrics
-
-- **Recall@k:** Percentage of test queries where the correct answer appears in top-k results
-- **MRR (Mean Reciprocal Rank):** Average of 1/rank for first correct result (higher is better; 1.0 = always rank-1)
-- **Latency:** Time to execute query (lexical + vector search + RRF fusion)
-- **Token savings:** Tokens used for surgical chunk vs full-file reads
-
-### Query Difficulties
-
-- **Easy (3–5 per suite):** Exact symbol names where recall-1 is guaranteed
-- **Medium (5–7 per suite):** Multi-token natural language descriptions
-- **Hard (4 per suite):** Semantic concepts with intentional vocabulary mismatch
-
-### Consistency
-
-All test suites use:
-- Same TF-IDF weighting and RRF parameters
-- Same Ollama model (`nomic-embed-text` v1)
-- Same demotion strategies (test files, examples, expressions)
-- Same exact-name boost multiplier (1.4×)
-
-Results are reproducible. Run `npm run test:embeddings --full-report` to regenerate all metrics for your machine.
+Released under the [MIT License](LICENSE). Copyright (c) 2026 MaquinaTech.
 
 ---
 
-**Read more:** See [PROMPT.md](./PROMPT.md) for detailed agent integration instructions.
+Built by [MaquinaTech](https://github.com/MaquinaTech) · [Issues](https://github.com/MaquinaTech/graph-indexer/issues) · [npm](https://www.npmjs.com/package/graph-indexer)