@iceinvein/code-intelligence-mcp 0.2.4 → 1.0.1

package/README.md

@@ -14,10 +14,14 @@ This server indexes your codebase locally to provide **fast, semantic, and struc
 
 Unlike basic text search, this server builds a local knowledge graph to understand your code.
 
-*   🔍 **Hybrid Search**: Combines **Tantivy** (keyword) + **LanceDB** (semantic vector) + **FastEmbed** (local embedding model).
-*   🚀 **Production First**: Ranking heuristics prioritize implementation code over tests and glue code (`index.ts`).
-*   🧠 **Developer Aware**: Handles common acronyms and casing (e.g., "db" matches "database" and "DBConnection").
-*   ⚡ **Fast & Local**: Written in **Rust**. Uses Metal GPU acceleration on macOS. Indexes are stored locally within your project.
+* 🔍 **Advanced Hybrid Search**: Combines **Tantivy** (keyword BM25) + **LanceDB** (semantic vector) + **Jina Code embeddings** (768-dim code-specific model) with Reciprocal Rank Fusion (RRF).
+* 🎯 **Cross-Encoder Reranking**: Always-on ORT-based reranker for precision result ranking.
+* 🧠 **Smart Context Assembly**: Token-aware budgeting with query-aware truncation that keeps relevant lines within context limits.
+* 📊 **PageRank Scoring**: Graph-based symbol importance scoring that identifies central, heavily-used components.
+* 🎓 **Learns from Feedback**: Optional learning system that adapts to user selections over time.
+* 🚀 **Production First**: Ranking heuristics prioritize implementation code over tests and glue code (`index.ts`).
+* 🔗 **Multi-Repo Support**: Index and search across multiple repositories/monorepos simultaneously.
+* ⚡ **Fast & Local**: Written in **Rust**. Uses Metal GPU acceleration on macOS. Parallel indexing with persistent caching.
 
 ---
 
@@ -47,16 +51,49 @@ Add to your `opencode.json` (or global config):
 
 ## Capabilities
 
-Available tools for the agent:
-
-| Tool | Description |
-| :--- | :--- |
-| `search_code` | **Primary Search.** Finds code by meaning ("how does auth work?") or structure ("class User"). |
-| `get_definition` | Retrieves the definition of a specific symbol. |
-| `find_references` | Finds all usages of a function, class, or variable. |
-| `get_call_hierarchy` | specifices upstream callers and downstream callees. |
-| `get_type_graph` | Explores inheritance and interface implementations. |
-| `get_usage_examples` | Returns real-world examples of how a symbol is used in the codebase. |
+Available tools for the agent (19 tools total):
+
+### Core Search & Navigation
+
+| Tool                       | Description                                                                                                                                                             |
+| :------------------------- | :---------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| `search_code`              | **Primary Search.** Finds code by meaning ("how does auth work?") or structure ("class User"). Supports query decomposition (e.g., "authentication and authorization"). |
+| `get_definition`           | Retrieves the full definition of a specific symbol with disambiguation support.                                                                                         |
+| `find_references`          | Finds all usages of a function, class, or variable.                                                                                                                     |
+| `get_call_hierarchy`       | Specifies upstream callers and downstream callees.                                                                                                                      |
+| `get_type_graph`           | Explores inheritance (extends/implements) and type aliases.                                                                                                             |
+| `explore_dependency_graph` | Explores module-level dependencies upstream or downstream.                                                                                                              |
+| `get_file_symbols`         | Lists all symbols defined in a specific file.                                                                                                                           |
+| `get_usage_examples`       | Returns real-world examples of how a symbol is used in the codebase.                                                                                                    |
+
+### Advanced Analysis
+
+| Tool                     | Description                                                                               |
+| :----------------------- | :---------------------------------------------------------------------------------------- |
+| `explain_search`         | Returns detailed scoring breakdown to understand why results ranked as they did.          |
+| `find_similar_code`      | Finds code semantically similar to a given symbol or code snippet.                        |
+| `trace_data_flow`        | Traces variable reads and writes through the codebase to understand data flow.            |
+| `find_affected_code`     | Finds code that would be affected if a symbol changes (reverse dependencies).             |
+| `get_similarity_cluster` | Returns symbols in the same semantic similarity cluster as a given symbol.                |
+| `summarize_file`         | Generates a summary of file contents including symbol counts, structure, and key exports. |
+| `get_module_summary`     | Lists all exported symbols from a module/file with their signatures.                      |
+
+### Testing & Documentation
+
+| Tool                    | Description                                                                                 |
+| :---------------------- | :------------------------------------------------------------------------------------------ |
+| `search_todos`          | Searches for TODO and FIXME comments to track technical debt.                               |
+| `find_tests_for_symbol` | Finds test files that test a given symbol or source file.                                   |
+| `search_decorators`     | Searches for TypeScript/JavaScript decorators (@Component, @Controller, @Get, @Post, etc.). |
+
+### Context & Learning
+
+| Tool               | Description                                                                     |
+| :----------------- | :------------------------------------------------------------------------------ |
+| `hydrate_symbols`  | Hydrates full context for a set of symbol IDs.                                  |
+| `report_selection` | Records user selection feedback for learning (call when user selects a result). |
+| `refresh_index`    | Manually triggers a re-index of the codebase.                                   |
+| `get_index_stats`  | Returns index statistics (files, symbols, edges, last updated).                 |
 
 ---
 
@@ -64,28 +101,46 @@ Available tools for the agent:
 
 The server supports semantic navigation and symbol extraction for the following languages:
 
-*   **Rust**
-*   **TypeScript / TSX**
-*   **JavaScript**
-*   **Python**
-*   **Go**
-*   **Java**
-*   **C**
-*   **C++**
+* **Rust**
+* **TypeScript / TSX**
+* **JavaScript**
+* **Python**
+* **Go**
+* **Java**
+* **C**
+* **C++**
 
 ---
 
-## Smart Ranking
+## Smart Ranking & Context Enhancement
+
+The ranking engine optimizes results for relevance using sophisticated signals:
+
+1. **PageRank Symbol Importance**: Graph-based scoring that identifies central, heavily-used components (similar to Google's PageRank).
+2. **Cross-Encoder Reranking**: Always-on ORT-based reranker applies deep learning to fine-tune result order.
+3. **Reciprocal Rank Fusion (RRF)**: Combines keyword, vector, and graph search results using statistically optimal rank fusion.
+4. **Query Decomposition**: Complex queries ("X and Y") are automatically split into sub-queries for better coverage.
+5. **Token-Aware Truncation**: Context assembly keeps query-relevant lines within token budgets using BM25-style relevance scoring.
+6. **Directory Semantics**: Implementation directories (`src`, `lib`, `app`) are boosted, while build artifacts (`dist`, `build`) and `node_modules` are penalized.
+7. **Test Penalty**: Test files (`*.test.ts`, `__tests__`) are ranked lower by default, but are boosted if the query intent implies testing.
+8. **Glue Code Filtering**: Re-export files (e.g., `index.ts`) are deprioritized in favor of the actual implementation.
+9. **JSDoc Boost**: Symbols with documentation receive a ranking boost, and examples are included in search results.
+10. **Learning from Feedback** (optional): Tracks user selections to personalize future search results.
+11. **Package-Aware Scoring** (multi-repo): Boosts results from the same package when working in monorepos.
+
+### Intent Detection
 
-The ranking engine optimizes results for relevance using several heuristics:
+The system detects query intent and adjusts ranking accordingly:
 
-1.  **Test Penalty**: Test files (`*.test.ts`, `__tests__`) are ranked lower by default, but are boosted if the query intent implies testing (e.g. "verify login").
-2.  **Glue Code Filtering**: Re-export files (e.g., `index.ts`) are deprioritized in favor of the actual implementation.
-3.  **Acronym Expansion**: Queries are normalized so "nav bar" matches `NavBar`, `Navigation`, and `NavigationBar`.
-4.  **Intent Detection**:
-    *   "struct User" → Boosts definitions.
-    *   "who calls login" → Triggers graph lookup.
-    *   "verify login" → Boosts test files.
+| Query Pattern     | Intent                    | Effect                                  |
+| ----------------- | ------------------------- | --------------------------------------- |
+| "struct User"     | Definition                | Boosts type definitions (1.5x)          |
+| "who calls login" | Callers                   | Triggers graph lookup                   |
+| "verify login"    | Testing                   | Boosts test files                       |
+| "User schema"     | Schema/Model              | Boosts schema/model files (50-75x)      |
+| "auth and authz"  | Multi-query decomposition | Splits into sub-queries, merges via RRF |
+
+For a deep dive into the system's design, see [System Architecture](SYSTEM_ARCHITECTURE.md).
 
 ---
 
@@ -93,12 +148,78 @@ The ranking engine optimizes results for relevance using several heuristics:
 
 Works without configuration by default. You can customize behavior via environment variables:
 
+### Core Settings
+
+```json
+"env": {
+  "BASE_DIR": "/path/to/repo",           // Required: Repository root
+  "WATCH_MODE": "true",                  // Watch for file changes (Default: true)
+  "INDEX_PATTERNS": "**/*.ts,**/*.go",   // File patterns to index
+  "EXCLUDE_PATTERNS": "**/node_modules/**",
+  "REPO_ROOTS": "/path/to/repo1,/path/to/repo2"  // Multi-repo support
+}
+```
+
+### Embedding Model
+
+```json
+"env": {
+  "EMBEDDINGS_BACKEND": "jinacode",      // jinacode (default), fastembed, hash
+  "EMBEDDINGS_DEVICE": "cpu",            // cpu or metal (macOS GPU)
+  "EMBEDDING_BATCH_SIZE": "32"
+}
+```
+
+### Context Assembly
+
+```json
+"env": {
+  "MAX_CONTEXT_TOKENS": "8192",          // Token budget for context (default: 8192)
+  "TOKEN_ENCODING": "o200k_base",        // tiktoken encoding model
+  "MAX_CONTEXT_BYTES": "200000"          // Legacy byte-based limit (fallback)
+}
+```
+
+### Ranking & Retrieval
+
+```json
+"env": {
+  "RANK_EXPORTED_BOOST": "0.1",          // Boost for exported symbols
+  "RANK_TEST_PENALTY": "0.1",            // Penalty for test files
+  "RANK_POPULARITY_WEIGHT": "0.05",      // PageRank influence
+  "RRF_ENABLED": "true",                 // Enable Reciprocal Rank Fusion
+  "HYBRID_ALPHA": "0.7"                  // Vector vs keyword weight (0-1)
+}
+```
+
+### Learning System (Optional)
+
+```json
+"env": {
+  "LEARNING_ENABLED": "false",           // Enable selection tracking (default: false)
+  "LEARNING_SELECTION_BOOST": "0.1",     // Boost for previously selected symbols
+  "LEARNING_FILE_AFFINITY_BOOST": "0.05" // Boost for frequently accessed files
+}
+```
+
+### Performance
+
+```json
+"env": {
+  "PARALLEL_WORKERS": "1",               // Indexing parallelism (default: 1 for SQLite)
+  "EMBEDDING_CACHE_ENABLED": "true",     // Persistent embedding cache
+  "PAGERANK_ITERATIONS": "20",           // PageRank computation iterations
+  "METRICS_ENABLED": "true",             // Prometheus metrics
+  "METRICS_PORT": "9090"
+}
+```
+
+### Query Expansion
+
 ```json
 "env": {
-  "WATCH_MODE": "true",          // Watch for file changes? (Default: false)
-  "EMBEDDINGS_DEVICE": "cpu",    // Force CPU if Metal fails (Default: metal on mac)
-  "INDEX_PATTERNS": "**/*.go",   // Add custom file types
-  "MAX_CONTEXT_BYTES": "50000"   // Limit context window
+  "SYNONYM_EXPANSION_ENABLED": "true",   // Expand "auth" → "authentication"
+  "ACRONYM_EXPANSION_ENABLED": "true"    // Expand "db" → "database"
 }
 ```
 
@@ -113,12 +234,14 @@ flowchart LR
   subgraph Server [Code Intelligence Server]
     direction TB
     Tools[Tool Router]
-    
+
     subgraph Indexer [Indexing Pipeline]
       direction TB
       Scan[File Scan] --> Parse[Tree-Sitter]
       Parse --> Extract[Symbol Extraction]
-      Extract --> Embed[FastEmbed Model]
+      Extract --> PageRank[PageRank Compute]
+      Extract --> Embed[Jina Code Embeddings]
+      Extract --> JSDoc[JSDoc/Decorator/TODO Extract]
     end
 
     subgraph Storage [Storage Engine]
@@ -126,17 +249,31 @@ flowchart LR
       SQLite[(SQLite)]
       Tantivy[(Tantivy)]
       Lance[(LanceDB)]
+      Cache[(Embedding Cache)]
+    end
+
+    subgraph Retrieval [Retrieval Engine]
+      direction TB
+      QueryExpand[Query Expansion]
+      Hybrid[Hybrid Search RRF]
+      Rerank[Cross-Encoder Reranker]
+      Signals[Ranking Signals]
+      Context[Token-Aware Assembly]
     end
 
     %% Data Flow
     Tools -- Index --> Scan
-    Embed --> SQLite
-    Embed --> Tantivy
+    PageRank --> SQLite
     Embed --> Lance
-    
-    Tools -- Query --> SQLite
-    Tools -- Query --> Tantivy
-    Tools -- Query --> Lance
+    Embed --> Cache
+    JSDoc --> SQLite
+
+    Tools -- Query --> QueryExpand
+    QueryExpand --> Hybrid
+    Hybrid --> Rerank
+    Rerank --> Signals
+    Signals --> Context
+    Context --> Tools
   end
 ```
 
@@ -144,6 +281,36 @@ flowchart LR
 
 ## Development
 
-1.  **Prerequisites**: Rust (stable), `protobuf`.
-2.  **Build**: `cargo build --release`
-3.  **Run**: `./scripts/start_mcp.sh`
+1. **Prerequisites**: Rust (stable), `protobuf`.
+2. **Build**: `cargo build --release`
+3. **Run**: `./scripts/start_mcp.sh`
+4. **Test**: `cargo test` or `EMBEDDINGS_BACKEND=hash cargo test` (faster, skips model download)
+
+### Quick Testing with Hash Backend
+
+For faster development iteration, use the hash embedding backend which skips model downloads:
+
+```bash
+EMBEDDINGS_BACKEND=hash BASE_DIR=/path/to/repo ./target/release/code-intelligence-mcp-server
+```
+
+### Project Structure
+
+```
+src/
+├── indexer/           # File scanning, parsing, symbol extraction
+├── storage/           # SQLite, Tantivy, LanceDB layers
+├── retrieval/         # Hybrid search, ranking, context assembly
+├── graph/             # PageRank, call hierarchy, type graphs
+├── handlers/          # MCP tool handlers
+├── server/            # MCP protocol routing
+├── tools/             # Tool definitions
+├── embeddings/        # Jina Code model wrapper
+├── reranker/          # Cross-encoder ORT implementation
+├── metrics/           # Prometheus metrics
+└── config.rs          # Environment-based configuration
+```
+
+## License
+
+MIT

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@iceinvein/code-intelligence-mcp",
-  "version": "0.2.4",
+  "version": "1.0.1",
   "description": "Code Intelligence MCP Server - Smart context for your LLM coding agent",
   "bin": {
     "code-intelligence-mcp": "bin/run.js"