codegraph-engine 3.0.0__tar.gz → 3.0.1.post1__tar.gz

{codegraph_engine-3.0.0/src/codegraph_engine.egg-info → codegraph_engine-3.0.1.post1}/PKG-INFO

@@ -1,14 +1,14 @@
 Metadata-Version: 2.4
 Name: codegraph-engine
-Version: 3.0.0
+Version: 3.0.1.post1
 Summary: Deep deterministic repository intelligence for AI coding agents (code, dependencies, databases, and runtime observations)
 Author: CodeGraph contributors
 License-Expression: MIT
-Project-URL: Homepage, https://github.com/raghurammrsd/CODE_GRAPH_MCP
-Project-URL: Repository, https://github.com/raghurammrsd/CODE_GRAPH_MCP
-Project-URL: Documentation, https://github.com/raghurammrsd/CODE_GRAPH_MCP/blob/main/docs/agent-brain.md
-Project-URL: Changelog, https://github.com/raghurammrsd/CODE_GRAPH_MCP/blob/main/CHANGELOG.md
-Project-URL: Issues, https://github.com/raghurammrsd/CODE_GRAPH_MCP/issues
+Project-URL: Homepage, https://github.com/raghurammrsd/CODEGRAPH_MCP
+Project-URL: Repository, https://github.com/raghurammrsd/CODEGRAPH_MCP
+Project-URL: Documentation, https://github.com/raghurammrsd/CODEGRAPH_MCP/blob/main/docs/agent-brain.md
+Project-URL: Changelog, https://github.com/raghurammrsd/CODEGRAPH_MCP/blob/main/CHANGELOG.md
+Project-URL: Issues, https://github.com/raghurammrsd/CODEGRAPH_MCP/issues
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
@@ -38,36 +38,37 @@ Dynamic: license-file
 <h1 align="center">CodeGraph MCP: Full-Stack Knowledge Graph & Semantic Intelligence for AI Coding Agents</h1>
 
 <p align="center">
-  <strong>Zero-Hallucination, AST-Verified Codebase Intelligence • Sub-15ms Live Watcher • 75% Context Token Reduction</strong><br>
-  <em>The ultimate Model Context Protocol (MCP) server for Cursor, Claude Code, GitHub Copilot, Antigravity, Cline, Windsurf & Codex.</em>
+  <strong>Deterministic AST-Verified Codebase Intelligence • Sub-15ms Live Watcher • Context Window Optimization</strong><br>
+  <em>Deterministic Model Context Protocol (MCP) server for Cursor, Claude Code, GitHub Copilot, Antigravity, Cline, Windsurf & Codex.</em>
 </p>
 
 <p align="center">
-  <a href="https://github.com/raghuram/CODE_GRAPH_MCP"><img src="https://img.shields.io/github/stars/raghuram/CODE_GRAPH_MCP?style=for-the-badge&logo=github&color=gold" alt="GitHub Stars" /></a>
+  <a href="https://github.com/raghurammrsd/CODEGRAPH_MCP"><img src="https://img.shields.io/github/stars/raghurammrsd/CODEGRAPH_MCP?style=for-the-badge&logo=github&color=gold" alt="GitHub Stars" /></a>
   <a href="https://pypi.org/project/codegraph-engine/"><img src="https://img.shields.io/badge/pypi-codegraph--engine-3776AB.svg?style=for-the-badge&logo=pypi" alt="PyPI: codegraph-engine" /></a>
-  <a href="src/codegraph/mcp/server.py"><img src="https://img.shields.io/badge/MCP-70%20Verified%20Tools-2ea043.svg?style=for-the-badge" alt="MCP Tools: 70 verified" /></a>
-  <a href="tests/"><img src="https://img.shields.io/badge/pytest-980%2B%20passed%20(100%25)-brightgreen.svg?style=for-the-badge&logo=pytest" alt="Tests: 980+ passed" /></a>
+  <a href="src/codegraph/mcp/server.py"><img src="https://img.shields.io/badge/MCP-97%20Verified%20Tools-2ea043.svg?style=for-the-badge" alt="MCP Tools: 97 verified" /></a>
+  <a href="tests/"><img src="https://img.shields.io/badge/pytest-1062%20passed%20(100%25)-brightgreen.svg?style=for-the-badge&logo=pytest" alt="Tests: 1062 passed" /></a>
   <a href="pyproject.toml"><img src="https://img.shields.io/badge/ruff-0%20errors-success.svg?style=for-the-badge" alt="Ruff: 0 errors" /></a>
-  <a href="src/codegraph/"><img src="https://img.shields.io/badge/mypy-strict%20(120%20files)-blue.svg?style=for-the-badge" alt="Mypy: strict" /></a>
-  <a href="https://github.com/raghuram/CODE_GRAPH_MCP/stargazers"><img src="https://img.shields.io/badge/Star%20on%20GitHub-loved%20by%20agents-yellow?style=for-the-badge" alt="Star us on GitHub" /></a>
+  <a href="src/codegraph/"><img src="https://img.shields.io/badge/mypy-strict%20(134%20files)-blue.svg?style=for-the-badge" alt="Mypy: strict" /></a>
 </p>
 
-> **Love CodeGraph MCP?** Please consider giving us a **Star on GitHub**! It helps AI developers discover deterministic, hallucination-free code intelligence for their pair programming agents.
+> CodeGraph MCP provides deterministic, evidence-backed repository intelligence through Abstract Syntax Trees, framework router hierarchies, database lineage, and runtime observation across 25 production pillars and 97 FastMCP tools.
 
 <p align="center">
-  <a href="https://raghurammrsd.github.io/CODE_GRAPH_MCP/"><strong>Documentation Site</strong></a> •
-  <a href="https://pypi.org/project/codegraph-engine/3.0.0/"><strong>PyPI Package</strong></a> •
+  <a href="https://raghurammrsd.github.io/CODEGRAPH_MCP/"><strong>Documentation Site</strong></a> •
+  <a href="https://pypi.org/project/codegraph-engine/3.0.1/"><strong>PyPI Package (v3.0.1)</strong></a> •
   <a href="#overview"><strong>Overview</strong></a> •
+  <a href="#the-25-production-pillars-of-codegraph-mcp"><strong>25 Pillars</strong></a> •
   <a href="#interactive-web-dashboard--vs-code-extension"><strong>Web Dashboard & VS Code</strong></a> •
-  <a href="#the-three-pillars-of-codegraph-mcp"><strong>The Three Pillars</strong></a> •
+  <a href="#multi-language-real-world-benchmark-results"><strong>Multi-Language Benchmarks</strong></a> •
+  <a href="#roblox--luau-intelligence-codegraph-roblox"><strong>Roblox & Luau</strong></a> •
   <a href="#2-quickstart-30-second-setup"><strong>Quickstart</strong></a> •
   <a href="#4-real-world-cli-outputs"><strong>CLI Outputs</strong></a> •
   <a href="#6-database-intelligence"><strong>Database Intelligence</strong></a> •
   <a href="#7-zero-friction-runtime-intelligence--static-reconciliation"><strong>Runtime Evidence</strong></a> •
   <a href="#8-git-aware-repository-intelligence"><strong>Git Intelligence</strong></a> •
   <a href="#measured-performance--real-metrics-benchmark"><strong>Benchmarks</strong></a> •
-  <a href="docs/agent-brain.md"><strong>70-Tool Reference</strong></a> •
-  <a href="https://github.com/raghurammrsd/CODE_GRAPH_MCP"><strong>GitHub</strong></a>
+  <a href="docs/agent-brain.md"><strong>97-Tool Reference</strong></a> •
+  <a href="https://github.com/raghurammrsd/CODEGRAPH_MCP"><strong>GitHub</strong></a>
 </p>
 
 ---
@@ -80,7 +81,7 @@ When AI coding agents (such as Claude Code, Cursor, or Antigravity) explore comp
 
 ### The Solution: CodeGraph MCP
 
-**CodeGraph MCP provides deterministic, compiler-grade repository intelligence through the Model Context Protocol.** Instead of guessing based on lexical approximations, the AI agent queries a local, persistent SQLite index for verified AST relationships, framework router trees, database lineages, and live runtime observations—resolved in sub-5ms latency.
+**CodeGraph MCP provides deterministic, evidence-backed repository intelligence through the Model Context Protocol.** Instead of guessing based on lexical approximations, the AI agent queries a local, persistent SQLite index for verified AST relationships, framework router trees, database lineages, and live runtime observations. When dynamic ambiguity occurs (such as untyped method receivers in Python or JS), relationships are explicitly tagged as `POSSIBLE` or `UNKNOWN` rather than inventing false facts.
 
 ```text
        ┌─────────────────────────────────────────────────────────────┐
@@ -92,10 +93,10 @@ When AI coding agents (such as Claude Code, Cursor, or Antigravity) explore comp
        ┌─────────────────────────────────────────────────────────────┐
        │                   CODEGRAPH MCP ENGINE                      │
        ├──────────────────────────────┬──────────────────────────────┤
-       │  AST Code Relationships      │  Framework Route Hierarchy   │
-       │  (Callers, Callees, DI)      │  (FastAPI, Django, Express)  │
+       │  AST Code Relationships      │  Framework & Network Graph   │
+       │  (Callers, Callees, DI)      │  (FastAPI, Django, Roblox)   │
        ├──────────────────────────────┼──────────────────────────────┤
-       │  Database Lineage & Schemas  │  Non-Invasive Dev Tracing    │
+       │  Database & DataStore Graph  │  Non-Invasive Dev Tracing    │
        │  (SQLAlchemy, Prisma, ORM)   │  (HTTP metrics, exceptions)  │
        └──────────────────────────────┴──────────────────────────────┘
                                       │
@@ -105,13 +106,13 @@ When AI coding agents (such as Claude Code, Cursor, or Antigravity) explore comp
 
 ### Core Architecture Capabilities
 
-- **Deterministic Evidence Guarantee**: Every returned entity and relationship is statically verified via Abstract Syntax Trees or explicitly flagged as `UNKNOWN` / `POSSIBLE`. CodeGraph MCP provides deterministic, evidence-backed repository intelligence across application code, databases, runtime behavior, and Git history.
+- **Deterministic Evidence Guarantee**: Every returned entity and relationship is statically verified via Abstract Syntax Trees (`AST_VERIFIED`, `FRAMEWORK_VERIFIED`, `ROJO_VERIFIED`) or explicitly flagged as `UNKNOWN` / `POSSIBLE`. CodeGraph MCP provides deterministic, evidence-backed repository intelligence across application code, databases, runtime behavior, and Git history.
 - **Sub-5ms Freshness Verification**: Monotonic commit tracking validates `git rev-parse HEAD` and porcelain status instantly, avoiding full-tree re-indexing on unchanged codebases.
 - **Context Window Optimization**: Yields 65% to 85% token reduction by returning structured, bounded source slices rather than entire file dumps.
 - **Zero-Friction Dev Interception (`codegraph run`)**: Wraps local development servers (e.g., `codegraph run npm run dev`, `codegraph run uvicorn main:app`) to capture real HTTP routes, latencies, and stack traces without application code changes.
 - **Multi-Agent Setup (`codegraph install`)**: Automatically detects, configures, and verifies integrations for Claude Code, Cursor, Antigravity, and Cline.
 
-> **Supported Languages & Frameworks:** Python (`FastAPI`, `Flask`, `Django`, `SQLAlchemy`, `PyTorch`, `Celery`, `LangChain`, `LlamaIndex`, `Ray`, `pytest`) and TypeScript / JavaScript (`.ts`, `.tsx`, `.js`, `.jsx`, `React`, `Next.js`, `NestJS`, `Express.js`, `Prisma`, `Drizzle`, `Mongoose`).
+> **Supported Languages & Frameworks:** Python (`FastAPI`, `Flask`, `Django`, `SQLAlchemy`, `PyTorch`), TypeScript / JavaScript (`React`, `Next.js`, `Express`, `NestJS`, `Prisma`), Roblox / Luau (`Rojo`, `Knit`, `DataStoreService`), Go (`Gin`, `Echo`, `net/http`), Rust (`Axum`, `Actix`, `Tokio`), Java (`Spring Boot`, `JPA`), and C/C++.
 
 <p align="center">
   <img src="docs/assets/codegraph_full_architecture.svg" alt="CodeGraph MCP Comprehensive Full-Stack Architecture Pipeline" width="950" />
@@ -123,25 +124,30 @@ When AI coding agents (such as Claude Code, Cursor, or Antigravity) explore comp
 
 ## Measured Performance & Real Metrics Benchmark
 
-CodeGraph MCP has been systematically benchmarked across 50 real-world engineering tasks and enterprise repositories to quantify token consumption, hallucination suppression, and investigation latency:
-
-| Performance Metric | Unassisted AI Agents (Raw Grep / File Dumps) | CodeGraph MCP Engine | Real Improvement |
-| :--- | :---: | :---: | :---: |
-| **Hallucination / Unsupported Claims** | 18.5% – 34.0% false assumptions | **0.0%** (AST / Framework verified) | **100% eliminated** |
-| **Context Window Consumption** | 4,500 – 18,200 tokens / task | **350 – 620 tokens / task** | **72% – 85% token savings** |
-| **Exploration Tool Calls** | 164 total tool calls | **71 tool calls** | **57% fewer tool calls** |
-| **Investigation Latency** | 14.8s average exploration | **4.8s total exploration** | **68% faster investigation** |
-| **Incremental File Reindexing** | Full scan required (1.2s – 6.5s) | **< 15ms per file (`codegraph watch`)** | **98% faster live sync** |
-| **Repository Freshness Check** | 450ms – 2,100ms disk stat checks | **< 5ms (Git commit fast path)** | **99% faster checks** |
-| **Symbol Grounding & Resolution** | Manual file scanning | **< 2ms in-memory SQLite** | **Sub-millisecond resolution** |
-| **Automated Test Suite Quality** | — | **980+ passed tests (100% pass rate)** | **Zero regressions** |
+Performance and retrieval accuracy are verified across two empirical evaluation suites: a **32-task agent navigation simulation** ([`src/codegraph/tool_selection_eval.py`](src/codegraph/tool_selection_eval.py)) measuring agent trajectory efficiency, and a **50-task diagnostic benchmark** ([`benchmarks/run_v21_eval.py`](benchmarks/run_v21_eval.py)) evaluating multi-file recall, coverage, and context boundaries:
+
+| Performance Metric | Unassisted AI Agents (Raw Grep / File Dumps) | CodeGraph MCP Engine | Measured Result | Evaluation Suite |
+| :--- | :---: | :---: | :---: | :---: |
+| **Unsupported Relationship Claims** | 18.5% – 34.0% false edges | **0.0%** (AST / Framework verified) | **100% eliminated** | 32-Task Navigation Eval |
+| **Exploration Tool Calls** | 164 total tool calls (~5.1 / task) | **71 tool calls** (~2.2 / task) | **56.7% fewer tool calls** | 32-Task Navigation Eval |
+| **Context Consumption (Prompt Tokens)** | 3,000 – 12,000+ tokens / task | **~510 tokens** avg payload | **72% – 85% token savings** | 32-Task Navigation Eval |
+| **Direct File Token Reduction** | Full file reads required | Bounded slices via `get_file` | **41.8% token reduction** | 50-Task Retrieval Benchmark |
+| **Multi-File Context Reduction** | 3,000 – 12,000+ tokens / task | **~510 tokens** avg payload | **72% – 85% token reduction** | 32-Task Navigation Eval |
+| **Task Coverage & Symbol Recall** | Baseline lexical match | **89.0% coverage / 72.5% recall** | **Verified ground truth** | 50-Task Retrieval Benchmark |
+| **In-Memory SQLite WAL Query** | Full rescan required (1.2s – 6.5s) | **< 15ms per query** | **Permanent WAL concurrency** | Persistent MCP Server Daemon |
+| **Binary CSR Pathfinding** | Linear graph scan | **< 1ms traversal** | **Microsecond CSR search** | `fast_graph_path` Traversal |
+| **CLI Cold Invocation Latency** | — | **~265ms total turnaround** | **Includes Python startup** | One-off CLI Subcommands |
+| **Single-File Full Re-index (Cold CLI)** | Full rescan required (4.4s) | **3.665s** (2,504 files) | **16.9% faster** | 4-Tier Stress Benchmark |
+| **Repository Freshness Check** | 450ms – 2,100ms disk stat checks | **< 5ms (Git commit fast path)** | **99% faster checks** | Git Fast Path Check |
+| **Symbol Grounding & Resolution** | Manual file scanning | **< 2ms in-memory SQLite** | **Sub-millisecond resolution** | SQLite Indexed Lookup |
+| **Automated Test Suite Quality** | — | **1,062 passed tests (100% pass rate)** | **Zero regressions** | Pytest CI/CD Suite |
 
 <p align="center">
   <img src="docs/assets/performance_comparison.svg" alt="CodeGraph MCP — Measured Context & Exploration Efficiency" width="850" />
 </p>
 
 <p align="center">
-  <img src="docs/assets/large_repo_scaling.svg" alt="CodeGraph MCP — Large Repository Scaling Across 100k, 500k, 1M LOC" width="850" />
+  <img src="docs/assets/large_repo_scaling.svg" alt="CodeGraph MCP — Large Repository Scaling up to 2,504 Files / ~120k LOC" width="850" />
 </p>
 
 ---
@@ -176,7 +182,7 @@ The CodeGraph VS Code extension brings deterministic repository intelligence dir
 ```bash
 # Package and install the extension
 cd vscode-extension
-code --install-extension codegraph-3.0.0.vsix
+code --install-extension codegraph-3.0.1.vsix
 ```
 
 Features included in the VS Code sidebar:
@@ -198,6 +204,14 @@ CodeGraph MCP natively parses AI/ML architectures and agent pipelines into deter
 - **LangChain LCEL Pipelines**: Tracks pipe syntax (`prompt | model | parser`) as executable pipeline dataflow (`CHAINS_TO`).
 - **Distributed Ray Tasks**: Detects `@ray.remote` actor decorators and `task.remote()` invocations (`DISPATCHES_RAY_TASK`).
 
+### Roblox & Luau Intelligence (`codegraph roblox`)
+First-class repository intelligence for Roblox game architectures (`.lua`, `.luau`, and `roblox-ts`):
+- **Native Luau Parser**: Extracts local/global functions, colon methods (`function Service:Init()`), dot methods (`function Module.Func()`), table-assigned methods (`Service.Method = function(...)`), module table returns, `return table.freeze(Module)`, and Luau `type` / `export type` declarations.
+- **Rojo DataModel Mapping (`default.project.json`)**: Maps virtual Roblox paths (`ReplicatedStorage`, `ServerScriptService`, `StarterPlayerScripts`, `Packages`, `script.Parent`) to physical files on disk with `ROJO_VERIFIED` provenance (`REQUIRES_MODULE`).
+- **Client $\leftrightarrow$ Server Network Graph**: Traces `RemoteEvent:FireServer(...)` $\to$ `OnServerEvent:Connect(handler)` and `RemoteFunction:InvokeServer(...)` $\to$ `OnServerInvoke = handler` through canonical Remote nodes via `CLIENT_DISPATCHES_REMOTE` and `SERVER_HANDLES_REMOTE`.
+- **Knit, Flamework & Persistence**: Tracks `Knit.CreateService` / `Knit.GetService`, Flamework `@Service` / `@Controller` / `Dependency<T>`, and `DataStoreService:GetDataStore` (`GetAsync`, `SetAsync`, `UpdateAsync`) + `ProfileService` (`CONFIGURES_PERSISTENCE`, `READS_PERSISTENCE`, `WRITES_PERSISTENCE`).
+- **Dedicated CLI Inspection**: `codegraph roblox remotes`, `codegraph roblox modules`, and `codegraph roblox routes`.
+
 ### Pillar 1: The Unified Full-Stack Bridge (`codegraph api-drift`)
 Bridges frontend client fetchers and backend API handlers across languages without manual tracing:
 - **Client Route Extraction**: Statically parses React / Next.js / Vue / Nuxt `fetch<T>()`, `axios.get<T>()`, `useSWR<T>()`, `useQuery<T>()`, and `$fetch<T>()` alongside TypeScript request/response interfaces.
@@ -218,69 +232,217 @@ Zero-heat, real-time file system monitoring with sub-15ms incremental reindexing
 - **Sub-15ms Incremental Reindexing**: Bypasses full-disk traversal; only re-indexes modified files (`Indexer.reindex_paths`) and advances generation counters.
 - **Instant In-Memory Cache Busting**: Automatically purges LRU memory caches (`_PARSE_CACHE`, `_GRAPH_CACHE`) and SQLite context caches upon file mutation.
 
-## 1. What's New in v3.0.0 (Git-Aware Intelligence)
+## 1. What's New in v3.0.1: 25 Production Pillars & 97 Verified FastMCP Tools
 
-Version `3.0.0` introduces compiler-grade **Git-Aware Repository Intelligence**, allowing AI agents and CI/CD pipelines to understand how code evolves across branches, commits, and working tree edits:
+CodeGraph **v3.0.1** is the production-grade codebase intelligence engine for AI coding agents, providing deterministic, source-verified AST facts, microsecond Compressed Sparse Row (CSR) graph pathfinding, and sub-15ms live file synchronization across 7 major programming languages.
 
-| Capability | CLI Command | MCP Tool | How It Solves Agent Failure Modes |
-| :--- | :--- | :--- | :--- |
-| **Working-Tree Freshness** | `codegraph git-state` | `get_git_state` | Tracks branch, HEAD vs indexed commit, modified/staged files with sub-millisecond status caching. Surfaces `CLEAN`, `DIRTY`, `STALE`, `REINDEXING`, `ERROR`. |
-| **Structural AST Diff** | `codegraph git-diff [base] [head]` | `compare_git` | Semantic diff across Git revisions: identifies added/removed/modified functions, changed parameter signatures, and affected routes—not merely raw line diffs. |
-| **Deep Impact & Visual Tree** | `codegraph git-impact --tree` | `get_change_impact` | Traverses downstream callers, callees, framework routes, DB writers, and affected test suites with token-bounded ranking and terminal ASCII tree visualization. |
-| **Semantic Merge Conflicts** | `codegraph git-conflicts [base] [head]` | `detect_semantic_conflicts` | Detects silent contract breaks before merge: invoking functions or route handlers that were deleted or modified on the target branch. |
-| **Context Freshness Gate** | `codegraph check-freshness [task]` | `check_context_freshness` | Determines whether previously compiled context remains `VALID`, `PARTIALLY_STALE`, or `STALE` without re-running full graph queries if unrelated files changed. |
-| **Deterministic Symbol History** | `codegraph symbol-history <sym>` | `trace_symbol_history` | Reconstructs the exact commit lifecycle of any symbol (introduced, modified, moved, renamed, or deleted) with confidence labels. |
+<p align="center">
+  <img src="docs/assets/codegraph_full_architecture.svg" alt="CodeGraph v3.0.1 Architecture Pipeline" width="100%" />
+</p>
+
+### Key Feature Highlights
+
+- **Microsecond CSR Traversal**: Traverses call chains and impact graphs across 100k+ edges in microseconds via binary Compressed Sparse Row matrices (`graph_csr.py`).
+- **97 Verified FastMCP Tools**: 100% audit pass rate across all registered FastMCP tools for Claude Code, Cursor, Antigravity, and Cline.
+- **65% to 85% Token Reduction**: Returns compact, bounded AST context packets (~510 tokens) rather than dumping entire multi-thousand-line files.
+- **7 Languages Native Support**: Python, TypeScript/JavaScript, Roblox/Luau, Go, Rust, Java, and C/C++.
+- **Zero Hallucinated Edges**: Every caller, route, and database relationship is compiler-verified (`AST_VERIFIED` / `FRAMEWORK_VERIFIED`).
+- **Universal Cross-Platform**: Native Windows `kernel32` process inspection, cp1252/UTF-8 terminal safety, and `python -m codegraph` execution out of the box.
+- **Sub-15ms Live Watcher**: Instant OS kernel push synchronization (macOS FSEvents, Linux inotify, Windows ReadDirectoryChangesW).
+- **Roblox & Luau Intelligence**: Client-server remote hopping, Rojo file tree mapping, and DataStore persistence lineage.
 
 ---
 
-## 1.1 What's New in v3.0.0
+### The 25 Production Pillars of CodeGraph MCP
+
+| Category | Pillar | Primary Tools | What It Does |
+|---|---|---|---|
+| **Code Intelligence** | **1. Multi-Language AST** | `resolve_symbol`, `batch_get_symbols` | Native AST extraction for 7 languages in <60ms. |
+| | **2. CSR Binary Graph** | `fast_graph_path`, `get_call_graph` | Microsecond pathfinding across binary CSR matrices. |
+| | **3. 97 FastMCP Tools** | 97 registered FastMCP endpoints | 100% verified tool suite spanning all capabilities. |
+| | **4. HTTP & RPC Routes** | `find_routes`, `list_routes` | FastAPI, Express, Spring Boot, Gin, Axum, Roblox Remotes. |
+| | **5. API Contract Drift** | `check_api_drift` | Statically matches frontend `fetch()` to backend routes. |
+| | **6. Dependency Injection** | `get_context`, `resolve_symbol` | Traces FastAPI `Depends`, Spring `@Autowired`, Gin middleware. |
+| | **7. Database Lineage** | `find_db_tables`, `get_db_impact` | Mapped SQLAlchemy, Prisma, JPA, SQLx, DataStore writers. |
+| **Safety & Testing** | **8. PR Blast Radius** | `analyze_change_impact`, `get_change_impact` | Downstream caller trees, impacted routes, and tests. |
+| | **9. Live Watcher** | `codegraph watch` | Kernel push events debounced in <15ms. |
+| | **10. Safe Refactoring** | `safe_rename`, `apply_semantic_patch` | Multi-file transactional patches with rollback safety. |
+| | **11. Multi-Agent Leases** | `claim_file_lease`, `release_file_lease` | Concurrency locks preventing swarm file collisions. |
+| | **12. Dead Code Detection** | `find_unreachable_code`, `find_dead_code` | Graph reachability traversal finding unused symbols. |
+| | **13. Taint Security** | `analyze_dataflow_taint` | Interprocedural dataflow tracking for injection flaws. |
+| | **14. Supply Chain CVE** | `analyze_supply_chain_cve_impact` | Maps package lockfile CVEs to internal code consumers. |
+| | **15. Repo Federation** | `federate_repositories` | Cross-repository HTTP and RPC service resolution. |
+| | **16. Test Scaffolding** | `generate_test_scaffolding` | Auto-generates unit test suites with mocked DB fixtures. |
+| | **17. LSP Bridge** | `codegraph lsp` | stdio LSP server with definition and caller CodeLens. |
+| **Operations & Storage** | **18. Agent Memory** | `store_agent_memory`, `query_agent_memory` | SQLite FTS5 experience store with sub-5ms BM25 search. |
+| | **19. Git Diff Freshness** | `get_git_state`, `compare_git` | Monotonic Git commit diffs & context invalidation. |
+| | **20. Index Self-Healing** | `repair_repository_index` | Automatic integrity checks and WAL rebuilds. |
+| | **21. SWE-bench Sandbox** | `evaluate_speculative_patch` | Isolated test execution harness for agent patches. |
+| | **22. PR Review Bot** | `generate_pr_review` | High-density PR review comments with risk badges. |
+| | **23. Web UI Dashboard** | `codegraph ui` | Browser visualizer on `127.0.0.1:8765`. |
+| | **24. Windows Portability** | `codegraph` CLI | Native Windows encoding, Win32 kernel32, and `python -m codegraph`. |
+| | **25. Universal Installer** | `codegraph install` | Auto-onboarding for Claude, Cursor, Antigravity, Cline. |
 
-Version `2.2.1` introduced runtime telemetry reconciliation, SQLite WAL concurrency, and multi-transport SSE resilience:
+---
 
-| Bottleneck Solved | How It Worked Before | CodeGraph MCP v3.0.0 Solution | Impact |
-| :--- | :--- | :--- | :--- |
-| **Runtime Telemetry Cold Start** | User had to manually configure OpenTelemetry exporters or Pino JSON log streaming pipelines. | **`codegraph run <command>`**: Transparent 1-line wrapper (`codegraph run npm run dev`, `codegraph run uvicorn main:app`) injecting non-invasive hooks (`NODE_OPTIONS` / `PYTHONSTARTUP`). | **Zero code changes**; streams HTTP route hits, latencies, and exception traces directly into `.codegraph/runtime.sqlite3`. |
-| **Database Concurrency (`database is locked`)** | Concurrent agent queries and background indexers could lock the SQLite database and raise crashes. | Enforced permanent **`WAL`** mode, **`synchronous = NORMAL`**, **`busy_timeout = 15000`** (15s), **`cache_size = -64000`** (64MB), and in-memory temporary storage. | Completely eliminates `database is locked` errors during parallel AI interrogation. |
-| **Index Freshness Verification Latency** | Full-repository file hash comparisons took seconds before queries on large codebases. | **Instant Git Commit Fast Path**: Validates `git rev-parse HEAD` match + clean `git status --porcelain`. Falls back to `st_mtime < idx_at` stat checks. | Reduces freshness verification from seconds to **`< 5ms`** on clean repositories. |
-| **Enterprise Monorepo Context Saturation** | Queries on 40,000-file monorepos could emit 50,000+ tokens for all routes or tables, blowing LLM context windows. | **Bounded Pagination**: Added `limit`, `offset`, `total_count`, and `has_more` to `list_routes` and `get_db_schema`. Added `--limit` / `--offset` to CLI `routes`. | Bounded context token consumption with strict pagination safeguards. |
-| **Client Disconnection (`exit status 0xffffffff`)** | Stdio MCP pipe termination caused permanent crash loops in agent IDEs on server updates or restarts. | **Multi-Transport Resiliency**: Added **`--transport sse`** (`--port`, `--host`) to `codegraph serve` and `codegraph mcp serve`. | Enables hot-reconnecting SSE HTTP transport alongside stdio for robust IDE bridges. |
+### Multi-Language Framework Benchmarks
+
+Evaluated against multi-layer framework fixtures (Gin HTTP, Axum + sqlx, Spring Boot + JPA, Express + React TSX, Rojo + DataStore) using CodeGraph v3.0.1 (97 FastMCP tools, SQLite WAL storage):
+
+| Language | Ecosystem / Framework | Indexing Time (Core AST) | SQLite DB Size | Files | Symbols | Edges | Avg Query Latency | Production Score |
+| :--- | :--- | :---: | :---: | :---: | :---: | :---: | :---: | :---: |
+| **Roblox / Luau** | Rojo / Knit / DataStore | **63 ms** (352 ms total) | 588 KB | 5 | 23 | 34 | 278 ms | **9.0 / 10** |
+| **Go** | Gin / GORM / net/http | **58 ms** (408 ms total) | 540 KB | 5 | 25 | 92 | 265 ms | **8.5 / 10** |
+| **TypeScript** | Express + React (TSX) | **81 ms** (378 ms total) | 560 KB | 5 | 16 | 101 | 268 ms | **8.5 / 10** |
+| **Java** | Spring Boot + JPA | **59 ms** (417 ms total) | 548 KB | 4 | 22 | 64 | 270 ms | **8.5 / 10** |
+| **Rust** | Axum + Tokio + sqlx | **48 ms** (312 ms total) | 484 KB | 5 | 14 | 29 | 264 ms | **8.5 / 10** |
+
+*Note on Latency:* Total CLI turnaround averages ~265 ms due to Python interpreter cold startup. The underlying SQLite WAL engine executes graph queries in **sub-15 ms**.
+
+---
+
+### Token Reduction & Context Window Optimization
+
+```text
+Without CodeGraph (Raw Grep / Full File Dumps):
+┌────────────────────────────────────────────────────────────────────────┐
+│ Entire Files Read (12,000+ Tokens)                                     │
+│ [====================================================================] │
+└────────────────────────────────────────────────────────────────────────┘
+
+With CodeGraph MCP (Targeted AST Slices & Evidence):
+┌───────────────────────────┐
+│ ~510 Tokens (72%–85% Saved│
+│ [======]                  │
+└───────────────────────────┘
+```
+
+- **65% to 85% Token Reduction**: Instead of transmitting 3,000 to 12,000 raw lines to the LLM, CodeGraph returns bounded, AST-verified context packets (~510 tokens average).
+- **56.7% Fewer Tool Calls**: Agents resolve multi-file call paths in an average of 2.2 tool calls versus 5.1 calls for naive unassisted agents.
+- **100% Elimination of Hallucinated Callers**: Grounded directly in AST coordinates, eliminating false edges entirely.
 
 ---
 
-## 2. Quickstart (30-Second Setup)
+## 2. Quickstart & Agent Installation
 
-### Step 1: Install the Package
+### Step 1: Install `codegraph-engine`
 
 ```bash
+# macOS / Linux
 pip install "codegraph-engine[mcp]"
+
+# Windows (PowerShell or Command Prompt)
+python -m pip install "codegraph-engine[mcp]"
+
+# Universal execution verification (works on all platforms even if Scripts/ is not on PATH)
+python -m codegraph --version
 ```
 
-### Step 2: Configure Your AI Coding Agents (`codegraph install`)
+> **Windows Portability:** CodeGraph v3.0.1 includes native Windows cp1252/UTF-8 terminal encoding safety, zero-dependency Win32 `kernel32` process inspection, and direct module-level execution via `python -m codegraph`. If the Windows `Scripts\` directory is not in your system `PATH`, executing `python -m codegraph <command>` works out of the box across PowerShell, CMD, and Windows Terminal.
+
+---
+
+### Step 2: Connect Your AI Coding Agents (`codegraph install --target`)
 
-CodeGraph MCP includes an interactive, idempotent onboarding installer ([`src/codegraph/installer.py`](src/codegraph/installer.py)) that detects installed AI coding agents (**Claude Code**, **Cursor**, **Antigravity**, **Codex CLI**, **Gemini CLI**, and **Cline**), configures `mcpServers.codegraph`, installs marker-bounded routing instructions (`<!-- CODEGRAPH:START -->` … `<!-- CODEGRAPH:END -->`), and verifies server health:
+CodeGraph MCP includes an automated, idempotent onboarding installer ([`src/codegraph/installer.py`](src/codegraph/installer.py)) that detects installed agents, configures `mcpServers.codegraph`, installs marker-bounded routing instructions (`<!-- CODEGRAPH:START -->` … `<!-- CODEGRAPH:END -->`), and verifies server health.
+
+#### Primary Target Commands (`--target`)
+
+Run `codegraph install` targeting your specific AI coding agent(s):
 
 ```bash
-# Interactive setup (detects installed agents, previews planned changes, asks confirmation)
-codegraph install
+# Target Claude Code (configures .mcp.json and CLAUDE.md)
+codegraph install --target claude --yes
+
+# Target Cursor (configures .cursor/mcp.json, .cursorrules, and .cursor/rules/codegraph.md)
+codegraph install --target cursor --yes
+
+# Target Google Antigravity / Gemini (configures .agents/mcp_config.json, AGENTS.md, and skills)
+codegraph install --target antigravity --yes
+
+# Target Cline / Roo Code (configures .cline/mcp_settings.json and .clinerules)
+codegraph install --target cline --yes
 
-# Non-interactive setup for all detected agents in the current project
-codegraph install --yes --target auto --location local
+# Target Codex CLI (configures .codex/mcp_config.json and AGENTS.md)
+codegraph install --target codex --yes
 
-# Preview exact file modifications without writing anything
-codegraph install --dry-run
+# Target Gemini CLI (configures .gemini/settings.json and GEMINI.md)
+codegraph install --target gemini --yes
+
+# Target multiple agents simultaneously
+codegraph install --target claude,cursor,antigravity --yes
+
+# Auto-detect all installed agents in the project / environment
+codegraph install --target auto --yes
+
+# Configure ALL supported agents at once
+codegraph install --target all --yes
 ```
 
+#### Installation Scopes (`--location`)
+
+```bash
+# Local Project Scope (Default): Configures the current repository directory
+codegraph install --target claude --location local --yes
+
+# Global Scope: Configures your user home directory (~/.claude.json, ~/.cursor/mcp.json, etc.)
+codegraph install --target cursor --location global --yes
+```
+
+#### Safe Previews, Manual Config & Repairs
+
+```bash
+# Dry-Run Preview: View planned file changes without modifying anything on disk
+codegraph install --target all --dry-run
+
+# Print Config Only: Output exact JSON snippet for manual pasting into GUI settings
+codegraph install --print-config claude
+codegraph install --print-config cursor
+codegraph install --print-config antigravity
+
+# Automatic Config Repair: Backs up and repairs corrupted or outdated MCP settings
+codegraph install --target auto --repair --yes
+
+# Clean Uninstall: Safely removes CodeGraph integration while preserving user files
+codegraph uninstall --target claude,cursor --yes
+
+# Uninitialize: Removes only the local repository index (.codegraph.sqlite3)
+codegraph uninit --yes
+```
+
+#### What `codegraph install` Configures Per Agent:
+
+| Target Agent (`--target`) | MCP Configuration File | Marker-Bounded Instructions | Skills & Rules |
+| :--- | :--- | :--- | :--- |
+| **`claude`** (Claude Code) | `.mcp.json` (local) / `~/.claude.json` (global) | `CLAUDE.md` | Marker section |
+| **`cursor`** (Cursor) | `.cursor/mcp.json` | `.cursorrules` | `.cursor/rules/codegraph.md` |
+| **`antigravity`** (Antigravity) | `.agents/mcp_config.json` | `AGENTS.md` | `.agents/rules/` & `.agents/skills/` |
+| **`cline`** (Cline / Roo Code) | `.cline/mcp_settings.json` | `.clinerules` | `.cline/rules/codegraph.md` |
+| **`codex`** (Codex CLI) | `.codex/mcp_config.json` | `AGENTS.md` | Marker section |
+| **`gemini`** (Gemini CLI) | `.gemini/settings.json` | `GEMINI.md` | Marker section |
+
+---
+
 ### Step 3: Initialize & Verify Your Project Index
 
 ```bash
 cd your-project
+
+# Initialize SQLite graph index (.codegraph.sqlite3 in WAL mode)
 codegraph init
+
+# Check index freshness (<5ms via Git commit fast path)
 codegraph status
-codegraph doctor
+
+# Verify database integrity and running MCP server processes
+codegraph doctor --database
+codegraph doctor --processes
 ```
 
 > **Dynamic Index Hot-Reloading:** If your AI coding agent launches `codegraph mcp serve` before you run `codegraph init`, you do **not** need to restart your IDE or MCP session. As soon as `codegraph init` or `codegraph index` creates or updates `.codegraph.sqlite3`, the running MCP server automatically detects the database on the next tool call and refreshes its in-memory graph cache (`get_repository_status(reload=True, reindex=True)` can also be invoked directly by the agent).
 
+---
+
 ### Step 4: Run With Zero-Friction Telemetry (`codegraph run`)
 
 Wrap your development server transparently to stream real HTTP routes, durations, and uncaught exceptions directly into CodeGraph MCP:
@@ -298,6 +460,18 @@ codegraph run python manage.py runserver
 
 ---
 
+### Step 5: Launch the Interactive Web Visualizer (`codegraph ui`)
+
+```bash
+# Launch interactive dashboard on http://127.0.0.1:8765
+codegraph ui
+
+# Custom port or headless server (no automatic browser launch)
+codegraph ui --port 9000 --no-browser
+```
+
+---
+
 ## 3. Core Architecture & Mental Model
 
 ```mermaid
@@ -337,7 +511,7 @@ EDITING        →  Native agent / IDE editing tools
 
 ## 4. Real-World CLI Outputs
 
-Below are exact, verifiable outputs produced by CodeGraph MCP v3.0.0:
+Below are exact, verifiable outputs produced by CodeGraph MCP v3.0.1:
 
 ### 1. Zero-Friction Runtime Interceptor (`codegraph run`)
 
@@ -352,13 +526,13 @@ $ codegraph run python3 -c "print('>> Dev server active on port 8000')"
 ```bash
 $ codegraph status .
 {
-  "repository": "/Users/raghuram/Documents/ChatGPT/MCP",
+  "repository": "/workspace/my-project",
   "freshness": "FRESH",
   "freshness_detail": "Index matches current repository state.",
   "files": 190,
   "chunks": 1965,
   "symbols": 1947,
-  "framework_routes": 0,
+  "framework_routes": 14,
   "graph_edges": 12712,
   "resource_profile": "BALANCED",
   "pressure_level": "NORMAL",
@@ -511,7 +685,7 @@ orders.user_id ──► users.id
 
 ## 7. Zero-Friction Runtime Intelligence & Static Reconciliation
 
-Static analysis proves what **can** happen structurally; runtime telemetry records what **was observed** during execution. CodeGraph MCP v3.0.0 brings them together transparently:
+Static analysis proves what **can** happen structurally; runtime telemetry records what **was observed** during execution. CodeGraph MCP v3.0.1 brings them together transparently:
 
 ```text
 STATIC GRAPH (AST + Framework + Dataflow + DB)
@@ -561,7 +735,7 @@ UNRESOLVED_REFERENCE / POSSIBLE_CALLS (status = "UNKNOWN" | "POSSIBLE")
 
 ## 8. Git-Aware Repository Intelligence & Merge Conflict Safety
 
-CodeGraph MCP v3.0.0 tracks the exact evolution of repository code across commits, branches, and working tree changes:
+CodeGraph MCP v3.0.1 tracks the exact evolution of repository code across commits, branches, and working tree changes:
 
 ```text
 Repository state
@@ -617,31 +791,35 @@ Automate change impact directly in your CI pipeline with `.github/workflows/code
 
 ### 4-Tier Scaling Summary (`54` → `2,504` Files)
 
-Recorded using [`benchmarks/run_v217_indexing_benchmark.py`](benchmarks/run_v217_indexing_benchmark.py) on macOS `arm64`, Python `3.13` with permanent SQLite WAL concurrency:
+Empirically measured using [`benchmarks/run_v217_indexing_benchmark.py`](benchmarks/run_v217_indexing_benchmark.py) on macOS `arm64`, Python `3.13` with permanent SQLite WAL concurrency:
 
-| Workload Tier | Files | Symbols | Graph Edges | Baseline Total | v3.0.0 Total | Improvement | Peak RSS | Peak WAL | Final WAL |
+| Workload Tier | Files | Symbols | Graph Edges | Baseline Total | v3.0.1 Measured | Measured Improvement | Peak RSS | Peak WAL | Final WAL |
 | :--- | ---: | ---: | ---: | ---: | ---: | :--- | ---: | ---: | ---: |
-| **Small** | `54` | `115` | `398` | `0.527 s` | `0.325 s` | **38.3% faster (`1.62x`)** | `46.25 MB` | `1.544 MB` | `0.0 MB` |
-| **Medium** | `304` | `615` | `2,248` | `2.564 s` | `1.613 s` | **37.1% faster (`1.59x`)** | `62.67 MB` | `4.098 MB` | `0.0 MB` |
-| **Large** | `1,004` | `2,015` | `7,428` | `8.730 s` | `5.296 s` | **39.3% faster (`1.65x`)** | `103.44 MB` | `5.033 MB` | `0.0 MB` |
-| **Stress** | `2,504` | `5,015` | `18,528` | `21.983 s` | `13.395 s` | **39.1% faster (`1.64x`)** | `180.89 MB` | `6.628 MB` | `0.0 MB` |
+| **Small** | `54` | `115` | `398` | `0.527 s` | `0.447 s` | **15.2% faster (`1.18x`)** | `48.00 MB` | `1.701 MB` | `0.0 MB` |
+| **Medium** | `304` | `615` | `2,248` | `2.564 s` | `2.159 s` | **15.8% faster (`1.19x`)** | `69.72 MB` | `4.082 MB` | `0.0 MB` |
+| **Large** | `1,004` | `2,015` | `7,428` | `8.730 s` | `7.157 s` | **18.0% faster (`1.22x`)** | `127.59 MB` | `5.190 MB` | `0.0 MB` |
+| **Stress** | `2,504` | `5,015` | `18,528` | `21.983 s` | `18.937 s` | **13.9% faster (`1.16x`)** | `233.59 MB` | `6.628 MB` | `0.0 MB` |
 
 ### Stress Tier (`2,504` Files) Phase Breakdown
 
-| Phase / Metric | Legacy Baseline | v3.0.0 Release | Measured Improvement |
+| Phase / Metric | Legacy Baseline | v3.0.1 Measured | Measured Improvement |
 | :--- | ---: | ---: | :--- |
-| **Total Indexing Time** | `21.983 s` | `13.395 s` | **39.1% faster (`1.64x`)** |
-| **Database Intelligence Pass** | `4.818 s` | `0.832 s` | **82.7% faster (`5.79x`)** |
-| **Post-Processing Phase** | `13.770 s` | `7.056 s` | **48.8% faster (`1.95x`)** |
-| **Symbol Resolution Phase** | `3.133 s` | `1.107 s` | **64.7% faster (`2.83x`)** |
-| **Single-File Incremental Update** | `4.408 s` | `2.063 s` | **53.2% faster (`2.14x`)** |
-| **Throughput (`files/sec`)** | `113.9 files/s` | `186.9 files/s` | **`+64.1%` throughput** |
+| **Total Indexing Time** | `21.983 s` | `18.937 s` | **13.9% faster (`1.16x`)** |
+| **Database Intelligence Pass** | `4.818 s` | `0.893 s` | **81.5% faster (`5.40x`)** |
+| **Post-Processing Phase** | `13.770 s` | `12.061 s` | **12.4% faster (`1.14x`)** |
+| **Symbol Resolution Phase** | `3.133 s` | `1.297 s` | **58.6% faster (`2.42x`)** |
+| **AST Parsing Phase** | `3.410 s` | `3.230 s` | **5.3% faster (`1.06x`)** |
+| **Cold CLI Single-File Re-index** | `4.408 s` | `3.665 s` | **16.9% faster (`1.20x`)** |
+| **Live In-Memory Incremental (`watch`)** | Full scan required | `< 15ms` / file | **Event-driven cache patch** |
+| **Throughput (`files/sec`)** | `113.9 files/s` | `132.2 files/s` | **`+16.1%` throughput** |
 | **Peak SQLite WAL Size** | `46.980 MB` | `6.628 MB` | **85.9% reduction (`7.09x` smaller)** |
 | **Final SQLite WAL Size** | `0.000 MB` | `0.000 MB` | **100% reclaimed (`TRUNCATE`)** |
 
+> **Note on Incremental Reindexing**: The **3.665 s** incremental figure measures a cold CLI invocation (`codegraph index .`) on the full 2,504-file repository, traversing file mtimes and checking Git diff state. In contrast, the active background daemon (`codegraph watch`) receives OS kernel filesystem events directly, parsing only the modified file's AST and patching SQLite in **< 15ms**.
+
 ![CodeGraph MCP — Measured Large-Repository Scaling](docs/assets/large_repo_scaling.svg)
 
-### 50-Task Production Benchmark Results (`v3.0.0`)
+### 50-Task Production Benchmark Results (`v3.0.1`)
 
 Evaluated across 50 production tasks and 10 categories via [`benchmarks/run_v21_eval.py`](benchmarks/run_v21_eval.py):
 
@@ -659,6 +837,8 @@ Evaluated across 50 production tasks and 10 categories via [`benchmarks/run_v21_
 
 ### 32-Task A/B Exploration Evaluation ([`src/codegraph/tool_selection_eval.py`](src/codegraph/tool_selection_eval.py))
 
+Evaluated across 32 agent navigation tasks comparing unassisted grep/file reading vs CodeGraph MCP tool calls:
+
 | Metric (32-Task Evaluation Suite) | Mode A (Unassisted Grep & File Reads) | Mode B (CodeGraph MCP) | Measured Improvement |
 | :--- | ---: | ---: | :--- |
 | **Total Tool Calls (32 Tasks)** | `164 calls` (`~5.1 / task`) | `71 calls` (`~2.2 / task`) | **`-56.7% fewer tool calls`** |
@@ -671,6 +851,18 @@ Evaluated across 50 production tasks and 10 categories via [`benchmarks/run_v21_
 
 ![CodeGraph MCP — Measured Context & Exploration Efficiency](docs/assets/performance_comparison.svg)
 
+### SWE-bench Comparative Benchmark Results (`benchmarks/swe_bench/`)
+
+Evaluated against standard software engineering problem statements comparing unassisted agents (grep + full file reads) vs CodeGraph MCP tool-assisted agents:
+
+| Metric | Baseline Mode (Grep / Read File) | CodeGraph MCP Mode | Measured Improvement |
+| :--- | ---: | ---: | :--- |
+| **Total Prompt Tokens Consumed** | `37,052 tokens` | `10,780 tokens` | **70.9% token reduction (`3.44x` efficiency)** |
+| **Average Turns to Resolution** | `8.0 turns` | `2.0 turns` | **75.0% turn reduction (`4.00x` faster)** |
+| **Direct Full-File Reads** | `14 files` | `0 files (0 bounded slices)` | **100.0% elimination of blind file reads** |
+| **Fault Localization Accuracy** | `50.0%` | `100.0%` | **`+50.0%` accuracy** |
+| **Resolution Status** | Partial / Stalled | `RESOLVED (100%)` | **Deterministic ground-truth symbol hit** |
+
 ---
 
 ## 10. Where CodeGraph MCP Fits
@@ -679,10 +871,10 @@ CodeGraph MCP works **alongside** your editor's language server (LSP), `ripgrep`
 
 Legend: `✓` supported • `◐` partial / workflow-dependent • `—` not supported
 
-| Capability | CodeGraph MCP (`v3.0.0`) | Editor LSP | Structural AST (`ast-grep`) | Lexical Search (`ripgrep`) | Remote Code Search (`Sourcegraph`) |
+| Capability | CodeGraph MCP (`v3.0.1`) | Editor LSP | Structural AST (`ast-grep`) | Lexical Search (`ripgrep`) | Remote Code Search (`Sourcegraph`) |
 | :--- | :---: | :---: | :---: | :---: | :---: |
 | **100% Local-First & Offline Operation** | ✓ | ✓ | ✓ | ✓ | — |
-| **Native MCP Server for AI Agents** | ✓ (14 default / 62 full) | — | ◐ | — | ✓ |
+| **Native MCP Server for AI Agents** | ✓ (14 default / 97 full) | — | ◐ | — | ✓ |
 | **Multi-Transport Support (stdio + SSE HTTP)** | ✓ | — | — | — | ◐ |
 | **Git-Aware AST Diffs & Freshness** | ✓ (6 Git tools) | — | — | — | ◐ |
 | **Zero-Friction Runtime Interceptor (`codegraph run`)** | ✓ | — | — | — | — |
@@ -716,9 +908,9 @@ Run `codegraph privacy .` at any time to audit the local database and verify tha
 
 ---
 
-## 12. MCP Tooling & Profiles (14 Default / 62 Full)
+## 12. MCP Tooling & Profiles (14 Default / 97 Full)
 
-By default, `create_server()` exposes the **14-tool `agent` profile** so AI coding agents receive a focused, non-overlapping tool surface. All 70 tools are available under `--profile full`.
+By default, `create_server()` exposes the **14-tool `agent` profile** so AI coding agents receive a focused, non-overlapping tool surface. All 97 verified tools are available under `--profile full`.
 
 ### Default `agent` Profile (14 High-Signal Tools)
 
@@ -748,7 +940,7 @@ By default, `create_server()` exposes the **14-tool `agent` profile** so AI codi
 | **`graph`** | **17** | Call-graph traversal, blast-radius impact (`analyze_impact`), and test discovery. |
 | **`minimal`** | **21** | Core interrogation plus `get_context`, `search_code`, `read_file`, and `verify_evidence`. |
 | **`developer`** | **34** | Interactive development with Git history (`get_file_history`, `get_recent_changes`) and retrieval planning. |
-| **`full`** | **62** | Complete capability surface including **11 Database tools**, **3 Runtime tools**, and **6 Git Intelligence tools** (`get_git_state`, `compare_git`, `get_change_impact`, `check_context_freshness`, `trace_symbol_history`, `detect_semantic_conflicts`). |
+| **`full`** | **97** | Complete capability surface including **18 Symbol tools**, **16 Call Graph tools**, **11 Database tools**, **9 Blast Radius tools**, **9 Multi-Agent & Memory tools**, **7 Refactoring & Patch tools**, **6 Route & Drift tools**, **6 Security & Rule tools**, and **9 File/Maintenance tools**. |
 
 ---
 
@@ -764,7 +956,7 @@ codegraph install --print-config claude                    # Print MCP JSON + ru
 codegraph install --dry-run                                # Preview planned file changes
 codegraph uninstall --yes                                  # Remove CodeGraph MCP agent integrations
 
-# Git-Aware Repository Intelligence (v3.0.0)
+# Git-Aware Repository Intelligence (v3.0.1)
 codegraph git-state .                                      # Track HEAD, working tree, and freshness (CLEAN/DIRTY/STALE)
 codegraph git-diff HEAD~1 HEAD                             # Semantic AST diff across commits or branches
 codegraph git-impact --tree                                # Deep downstream change impact with visual ASCII tree
@@ -772,7 +964,7 @@ codegraph git-conflicts main HEAD                          # Detect pre-merge se
 codegraph check-freshness "audit auth flow"                # Validate if compiled context is VALID or STALE
 codegraph symbol-history resolve_target                    # Trace deterministic symbol lifecycle across commits
 
-# Zero-Friction Runtime Interceptor (v3.0.0)
+# Zero-Friction Runtime Interceptor (v3.0.1)
 codegraph run npm run dev                                  # Wrap Node/Express/Next.js dev server
 codegraph run uvicorn main:app --reload                    # Wrap FastAPI/ASGI dev server
 codegraph run python manage.py runserver                   # Wrap Django dev server
@@ -793,7 +985,7 @@ codegraph doctor --processes                               # Inspect active MCP
 codegraph status .                                         # Show index freshness (sub-50ms Git fast path)
 codegraph doctor . --database --processes                  # Verify SQLite integrity, FKs, FTS, and memory
 codegraph privacy .                                        # Verify zero sensitive files indexed
-codegraph version                                          # Print CodeGraph MCP version (3.0.0)
+codegraph version                                          # Print CodeGraph MCP version (3.0.1)
 
 # Code, Graph, Routes & Context Interrogation
 codegraph search "authenticate" -r .                       # Search indexed symbols and text chunks
@@ -805,9 +997,24 @@ codegraph routes -r . --limit 25 --offset 0                # List routes with bo
 codegraph architecture -r .                                # Summarize repository architecture
 codegraph context "trace /api/v1/auth/login" -r .          # Compile token-budgeted ContextPacket
 
+# Dead Code & Zombie Route Detection
+codegraph dead-code .                                      # Audit zero-caller symbols, zombie routes & orphaned tables
+codegraph dead-code . --json                               # Output dead-code report as structured JSON
+
+# Embedded OpenTelemetry (OTLP/HTTP) Receiver
+codegraph otel-listen --port 4318                          # Listen for standard OTLP HTTP /v1/traces spans
+codegraph otel-listen --host 0.0.0.0 --port 4318           # Accept remote container telemetry streams
+
+# Language Server Protocol (LSP) Bridge
+codegraph lsp .                                            # Run stdio LSP server for VS Code / Neovim / Helix
+
+# Multi-File Transactional Semantic Patch Engine
+codegraph refactor patch patch.json --dry-run              # Preview patch diff & affected symbols (0 disk mutations)
+codegraph refactor patch patch.json                        # Apply patch atomically with syntax validation & rollback
+
 # MCP Server Subcommands
 codegraph serve .                                          # Start stdio MCP server (14 default tools)
-codegraph serve . --profile full                           # Start stdio MCP server with all 70 tools
+codegraph serve . --profile full                           # Start stdio MCP server with all 97 tools
 codegraph serve . --transport sse --port 8765              # Start SSE HTTP server on port 8765
 codegraph mcp serve . --transport sse                      # Alias for SSE MCP server
 codegraph mcp stop                                         # Stop active MCP processes
@@ -817,7 +1024,7 @@ codegraph mcp stop                                         # Stop active MCP pro
 
 ## 14. Documentation Map
 
-- **Deep Agent Brain & 70-Tool Reference**: [`docs/agent-brain.md`](docs/agent-brain.md)
+- **Deep Agent Brain & 97-Tool Reference**: [`docs/agent-brain.md`](docs/agent-brain.md)
 - **Compact Tool Capabilities Summary**: [`agent-rules/tool-capabilities-summary.md`](agent-rules/tool-capabilities-summary.md)
 - **Detailed Multi-Tool Capability Comparison**: [`docs/tool-comparison.md`](docs/tool-comparison.md)
 - **Antigravity Skill (`SKILL.md`)**: [`.agents/skills/codegraph/SKILL.md`](.agents/skills/codegraph/SKILL.md)
@@ -831,8 +1038,8 @@ codegraph mcp stop                                         # Stop active MCP pro
 ## 15. Contributing & License
 
 ```bash
-git clone https://github.com/raghurammrsd/CODE_GRAPH_MCP.git
-cd CODE_GRAPH_MCP
+git clone https://github.com/raghurammrsd/CODEGRAPH_MCP.git
+cd CODEGRAPH_MCP
 python3 -m venv .venv
 source .venv/bin/activate
 pip install -e ".[dev,mcp,system]"