diff --git a/.github/FUNDING.yml b/.github/FUNDING.yml
new file mode 100644
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--- /dev/null
+++ b/.github/FUNDING.yml
@@ -0,0 +1 @@
+ko-fi: hungpham55178
diff --git a/README.md b/README.md
index 7f4e584ef..62454c942 100644
--- a/README.md
+++ b/README.md
@@ -2,31 +2,149 @@
[](https://github.com/hungpham10/codegraph-rs/actions/workflows/ci.yml)
[](https://app.codspeed.io//hungpham10/codegraph-rs?utm_source=badge)
-[](https://codecov.io/gh/hungpham10/codegraph-rs)
+[](https://codecov.io/gh/hungpham10/codegraph-rs)
[](LICENSE)
-> Local-first code intelligence for AI agents. Built in Rust.
+> **Local-first semantic code graph for AI agents** — tree-sitter parsing, global symbol IDs, call chains with control-flow markers, served over MCP. Single **~58 MB** static binary.
-CodeGraph parses your codebase with tree‑sitter, builds a semantic graph where each symbol has a global ID and each function a call chain, and serves the graph to AI agents via the Model Context Protocol (MCP).
+CodeGraph parses your codebase with tree-sitter, builds a **semantic graph** where every symbol gets a global ID and every function has a **call chain** (markers + callee IDs), stores everything under `.codegraph/` (SQLite by default), and exposes the graph to AI agents — Claude Code, Cursor, Codex CLI, opencode, Hermes, Antigravity — over the Model Context Protocol (MCP).
-## Install
+Agents that consult the semantic graph instead of grepping the filesystem make **fewer tool calls**, **explore faster**, and **stay within context**.
-**Automatic (recommended)**
-
-- **Linux / macOS**: `curl -fsSL https://raw.githubusercontent.com/hungpham10/codegraph-rs/main/scripts/install.sh | sh`
-- **Windows (PowerShell)**: `irm https://raw.githubusercontent.com/hungpham10/codegraph-rs/main/scripts/install.ps1 | iex`
+## Why CodeGraph?
-*See the full installation guide at* [docs/specs/08-installer.md](docs/specs/08-installer.md).
+- **Fewer tool calls** — agents navigate call chains (`codegraph_flow`), not grep
+- **Local & fast** — full re-index 139 files in ~190 ms, nothing leaves your machine
+- **Works everywhere** — 14 languages, 6 storage backends, 24 MCP tools, one binary
+- **Semantic, not syntactic** — symbols have global IDs; edges derived from call chains with markers (`LOOP`, `IF_TRUE`, `RETURN`, …)
-## Quick start
+## ⚡ Quick Start
-```sh
+```bash
+# 1. Initialize and index your project
+cd ~/code/my-project
codegraph init
+
+# 2. Serve to your agent over MCP (stdio)
codegraph serve --mcp
+
+# ... or over Streamable HTTP (for remote/Docker)
+codegraph serve --mcp --http --addr 0.0.0.0:8123
+```
+
+The agent binds the workspace with `codegraph_init {"path": ...}` and gets tools like `codegraph_search_symbol`, `codegraph_flow`, `codegraph_callers`, `codegraph_impact`, `codegraph_context` — all querying over MCP.
+
+## 📊 Comparison — Why Not X?
+
+| Tool | Type | Local-First | Semantic Graph | MCP Native | Multi-Storage | Binary Size |
+|------|------|-------------|----------------|------------|---------------|-------------|
+| **CodeGraph** | Code graph + MCP | ✅ | ✅ (tree-sitter semgraph) | ✅ Built-in | ✅ 6 backends | ~58 MB |
+| Aider RepoMap | Repo map generator | ✅ | ❌ (ctags-based) | ❌ | ❌ | N/A |
+| Sourcegraph Cody | Cloud code search | ❌ (self-host) | ✅ (CodeQL) | Via extension | ❌ | N/A |
+| Bloop | Code indexer | ✅ | ❌ (search only) | ❌ | ❌ | ~30 MB |
+| CodeQL | Semantic analysis | ✅/Cloud | ✅ (QL queries) | ❌ | ❌ | Heavy |
+| Kythe | Code graph | ✅ | ✅ | ❌ | ❌ | Complex setup |
+| LSP servers | Per-language IDE | ✅ | Per-lang only | ❌ | ❌ | Per-lang |
+| ast-grep | Structural search | ✅ | ❌ (pattern match) | ❌ | ❌ | ~10 MB |
+| context7 | Docs MCP | ❌ | N/A | ✅ | ❌ | N/A |
+
+→ [Full comparison with decision matrix](docs/comparison.md)
+
+## 🎯 Key Features
+
+- **24 MCP tools** — `search_symbol`, `flow`, `callers`, `callees`, `impact`, `search_flow`, `context`, `references`, `diff`, `sandbox`, `mermaid`, and more
+- **14 languages** — TypeScript · TSX · JavaScript · Python · Go · Rust · Java · C · C++ · C# · Ruby · PHP · Scala · Swift · Lua
+- **6 storage backends** — SQLite (default), LMDB, Redis, Postgres, MySQL, Memory
+- **Semantic search** — opt-in fastembed (BGE-small) for hybrid KNN + keyword search
+- **Behavior sandbox** — JIT compile function groups + run against Rhai mocks
+- **Full re-index always** — watcher debounces changes, re-indexes completely (simpler, no stale state)
+
+## 📦 Install
+
+**Automatic (recommended)**
+
+```bash
+# Linux / macOS
+curl -fsSL https://raw.githubusercontent.com/hungpham10/codegraph-rs/main/scripts/install.sh | sh
+
+# Windows (PowerShell)
+irm https://raw.githubusercontent.com/hungpham10/codegraph-rs/main/scripts/install.ps1 | iex
```
-## Documentation
+**Other options**: [Homebrew](https://github.com/hungpham10/homebrew-codegraph) • [AUR](https://aur.archlinux.org/packages/codegraph-rs-bin) • [.deb/.rpm](https://github.com/hungpham10/codegraph-rs/releases/latest) • `cargo install --git https://github.com/hungpham10/codegraph-rs codegraph`
+
+[Full install guide →](docs/specs/08-installer.md)
+
+## 🔧 Configuration (Essentials)
+
+```toml
+# .codegraph/config.toml
+[storage]
+type = "sqlite" # or lmdb, redis, postgres, mysql, memory
+
+[embedding]
+# backend = "fastembed" # enable semantic/hybrid search
+```
+
+[Full config reference →](docs/configuration.md) | [Storage backends →](docs/storage-backends.md) | [Semantic search →](docs/semantic-search.md)
+
+## 🏗️ Architecture
+
+```
+files → tree-sitter (rayon) → semgraph (global IDs + chains)
+ → GraphIndex (2 engines + pluggable storage)
+ → MCP server (24 tools) → AI Agent
+```
+
+[Architecture deep-dive →](docs/architecture.md)
+
+## 📚 Documentation Map
+
+| Topic | File |
+|-------|------|
+| Architecture & Pipeline | `docs/architecture.md` |
+| Extraction & Languages | `docs/specs/04-extraction.md` |
+| Storage & GraphIndex | `docs/specs/03-db-layer.md` |
+| MCP Server & Tools | `docs/specs/07-mcp-server.md` |
+| CLI & Watcher | `docs/specs/09-cli-watcher.md` |
+| Semgraph Model | `docs/specs/02-core-types.md` |
+| Installer Details | `docs/specs/08-installer.md` |
+| **Full Comparison** | `docs/comparison.md` |
+| Configuration Reference | `docs/configuration.md` |
+| Storage Backends | `docs/storage-backends.md` |
+| Semantic Search | `docs/semantic-search.md` |
+| Why Rust (Rewrite Story) | `docs/why-rust.md` |
+| Development Guide | `docs/development.md` |
+
+## 🤝 Contributing
+
+```bash
+cargo build --workspace
+cargo test --workspace
+cargo clippy --workspace --all-targets -- -D warnings
+cargo fmt --all
+```
+
+See [Development Guide](docs/development.md) for feature flags, per-crate tests, and release process.
+
+## Sponsors
+
+You can buy me a coffee by sending me money by MOMO
+
+
+ 
+
+
+
+Or send to me through
+[](https://ko-fi.com)
+
+## License
+
+MIT. See [LICENSE](LICENSE).
+
+## Acknowledgments
-- Architecture overview: [docs/architecture.md](docs/architecture.md)
-- Detailed installation guide: [docs/specs/08-installer.md](docs/specs/08-installer.md)
-- Full reference (configuration, CLI, MCP tools) – see the original README for comprehensive information.
+- Original TypeScript implementation by [@colbymchenry](https://github.com/colbymchenry)
+- `tree-sitter` and all language grammar authors
+- `rusqlite`, `notify`, `clap`, `tokio`, `rayon`, `ignore`, `dashmap`, `parking_lot`
diff --git a/assets/sponsor/MOMO.JPG b/assets/sponsor/MOMO.JPG
new file mode 100644
index 000000000..9b02c1de6
Binary files /dev/null and b/assets/sponsor/MOMO.JPG differ
diff --git a/docs/comparison.md b/docs/comparison.md
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--- /dev/null
+++ b/docs/comparison.md
@@ -0,0 +1,237 @@
+# Comparison — CodeGraph vs Alternatives
+
+This document provides a detailed comparison of CodeGraph with other tools in the code intelligence and AI agent tooling space.
+
+## Quick Comparison Table
+
+| Tool | Category | Local-First | Semantic Graph | MCP Native | Multi-Storage | Binary Size | Best For |
+|------|----------|-------------|----------------|------------|---------------|-------------|----------|
+| **CodeGraph** | Code graph + MCP | ✅ | ✅ (tree-sitter semgraph) | ✅ Built-in | ✅ 6 backends | ~58 MB | Local-first AI agents needing full semantic graph |
+| **Aider RepoMap** | Repo map generator | ✅ | ❌ (ctags-based) | ❌ | ❌ | N/A | Aider users wanting quick repo overview |
+| **Sourcegraph Cody** | Cloud code search | ❌ (self-host option) | ✅ (CodeQL) | Via extension | ❌ | N/A | Enterprise multi-repo search |
+| **Bloop** | Code indexer | ✅ | ❌ (search only) | ❌ | ❌ | ~30 MB | Fast local code search |
+| **CodeQL** | Semantic analysis | ✅/Cloud | ✅ (QL queries) | ❌ | ❌ | Heavy | Security auditing, variant analysis |
+| **Kythe** | Code graph | ✅ | ✅ | ❌ | ❌ | Complex setup | Large-scale build-integrated graphs |
+| **LSP servers** (rust-analyzer, clangd, etc.) | Per-language IDE | ✅ | Per-lang only | ❌ | ❌ | Per-lang | IDE integration per language |
+| **ast-grep** | Structural search | ✅ | ❌ (pattern match) | ❌ | ❌ | ~10 MB | AST pattern matching/replace |
+| **context7** | Docs MCP | ❌ | N/A | ✅ | ❌ | N/A | API/documentation context |
+
+---
+
+## Detailed Breakdown
+
+### CodeGraph (This Project)
+
+**What it is**: A local-first semantic code graph built on tree-sitter that serves AI agents via the Model Context Protocol (MCP).
+
+**Strengths**:
+- **True semantic graph**: Symbols have global IDs; call chains capture control flow (LOOP, IF_TRUE, RETURN, etc.)
+- **MCP-native**: 24 tools exposed directly — no wrapper needed
+- **Multi-storage**: SQLite (default), LMDB, Redis, Postgres, MySQL, in-memory
+- **Single binary**: ~58 MB with all backends + embedding runtime bundled
+- **14 languages** with full extraction: TypeScript, TSX, JavaScript, Python, Go, Rust, Java, C, C++, C#, Ruby, PHP, Scala, Swift, Lua
+- **Optional semantic search**: fastembed (BGE-small) for hybrid KNN + keyword search
+- **Behavior sandbox**: JIT compile functions + run against Rhai mocks
+- **Full re-index always**: Simpler, no stale state; 139 files in ~190 ms
+
+**Trade-offs**:
+- No incremental sync (by design — full re-index on change)
+- Requires MCP-compatible agent (Claude Code, Cursor, Codex, opencode, Hermes, Antigravity)
+- Postgres/MySQL schema applied manually (no auto-migrations)
+
+---
+
+### Aider RepoMap
+
+**What it is**: A repository map generator integrated into Aider (AI pair programmer). Uses ctags + tree-sitter to create a condensed representation of the codebase for LLM context.
+
+**Strengths**:
+- Tightly integrated with Aider's editing workflow
+- Fast, lightweight
+- Works with 50+ languages via ctags
+
+**Weaknesses vs CodeGraph**:
+- Not a persistent semantic graph — regenerates per session
+- No global symbol IDs or call chains
+- No MCP server — only works within Aider
+- No storage backends, no semantic search
+- Ctags-based (less precise than tree-sitter extraction)
+
+**When to choose**: You use Aider exclusively and want zero-setup repo context.
+
+---
+
+### Sourcegraph Cody
+
+**What it is**: Enterprise code search + AI assistant. Uses CodeQL for semantic analysis, offers cloud and self-hosted options.
+
+**Strengths**:
+- Cross-repository search at scale
+- CodeQL-powered semantic queries
+- Enterprise features (RBAC, audit logs, compliance)
+- IDE integrations (VS Code, JetBrains)
+
+**Weaknesses vs CodeGraph**:
+- Cloud-first (self-host is complex)
+- Heavy infrastructure (PostgreSQL, Redis, Kafka, etc.)
+- Not a local-first single binary
+- No native MCP server (uses proprietary protocol)
+- Expensive for teams
+
+**When to choose**: Enterprise needing multi-repo search, compliance, and can invest in infrastructure.
+
+---
+
+### Bloop
+
+**What it is**: Fast Rust-based code indexer and search tool. Focuses on regex/keyword search with some semantic awareness.
+
+**Strengths**:
+- Very fast indexing and search
+- Rust-based, single binary (~30 MB)
+- Local-first
+
+**Weaknesses vs CodeGraph**:
+- No semantic graph — no global IDs, no call chains
+- No MCP server
+- No semantic search (embeddings)
+- Limited language extraction depth
+
+**When to choose**: You only need fast code search, not semantic graph for AI agents.
+
+---
+
+### CodeQL
+
+**What it is**: Semantic code analysis engine from GitHub. Uses a query language (QL) to find vulnerabilities and patterns.
+
+**Strengths**:
+- Deep semantic analysis via QL
+- Industry standard for security research
+- Variant analysis (find similar bugs)
+- GitHub Advanced Security integration
+
+**Weaknesses vs CodeGraph**:
+- Query-based, not graph-native — you write QL, don't traverse a graph
+- Heavy (Java-based, large download)
+- No MCP server
+- No persistent graph storage for agent queries
+- Steep learning curve (QL language)
+
+**When to choose**: Security auditing, variant analysis, compliance — not for AI agent context.
+
+---
+
+### Kythe
+
+**What it is**: Google's language-agnostic code graph platform. Extracts facts from builds, stores in a graph.
+
+**Strengths**:
+- Language-agnostic (supports 15+ languages)
+- Build-system integrated (Bazel, Gradle, etc.)
+- Scales to massive codebases (Google-scale)
+
+**Weaknesses vs CodeGraph**:
+- Complex setup (requires build integration)
+- No MCP server
+- No single binary — distributed services
+- Not designed for local AI agent use
+- Steep operational overhead
+
+**When to choose**: Large org with build infrastructure wanting cross-language code graph.
+
+---
+
+### LSP Servers (rust-analyzer, clangd, pyright, etc.)
+
+**What it is**: Language Server Protocol implementations per language. Provide IDE-grade semantic analysis.
+
+**Strengths**:
+- Best-in-class per-language semantics
+- IDE integration (completion, goto definition, refactor)
+- Local-first
+
+**Weaknesses vs CodeGraph**:
+- Per-language only — no cross-language graph
+- No unified symbol IDs across languages
+- No MCP server (though some bridges exist)
+- No persistent graph storage
+- Not designed for AI agent consumption
+
+**When to choose**: IDE development — not for AI agent context.
+
+---
+
+### ast-grep
+
+**What it is**: Structural search and replace using tree-sitter patterns. Like grep but AST-aware.
+
+**Strengths**:
+- 30+ languages via tree-sitter
+- Pattern matching on AST nodes
+- Fast, single binary (~10 MB)
+- Local-first
+
+**Weaknesses vs CodeGraph**:
+- No persistent graph — ephemeral pattern matching
+- No global symbol IDs or call chains
+- No MCP server
+- No semantic search (embeddings)
+- Not a queryable index
+
+**When to choose**: One-off structural search/replace, codemods — not for persistent AI context.
+
+---
+
+### context7 (Upstash)
+
+**What it is**: MCP server for documentation and API context. Not a code graph.
+
+**Strengths**:
+- MCP-native
+- Good for API/docs lookup
+
+**Weaknesses vs CodeGraph**:
+- No code analysis whatsoever
+- Cloud-only
+- Different use case entirely
+
+**When to choose**: Agents need API documentation context, not codebase understanding.
+
+---
+
+## Decision Matrix
+
+| Your Need | Recommended Tool |
+|-----------|------------------|
+| Local AI agent + semantic graph + MCP | **CodeGraph** |
+| Aider user, quick repo map | Aider RepoMap |
+| Enterprise multi-repo search + compliance | Sourcegraph Cody |
+| Fast local code search only | Bloop |
+| Security auditing, variant analysis | CodeQL |
+| Massive monorepo with build integration | Kythe |
+| IDE development (completion, refactor) | LSP servers |
+| Structural search/replace, codemods | ast-grep |
+| API documentation for agents | context7 |
+
+---
+
+## Methodology
+
+This comparison is based on:
+- Public documentation and GitHub repos (as of 2026)
+- Feature matrices from project READMEs
+- Architecture descriptions (local vs cloud, graph vs search vs pattern-match)
+- No hands-on benchmarking — performance claims are from respective projects
+
+**Missing from this table**: Greptile (cloud PR review), Continue.dev (IDE extension), Cursor indexing (IDE-tied), Glean (enterprise search), semgrep (linting), bito/DeepSource (cloud review). These serve different primary use cases.
+
+---
+
+## See Also
+
+- [README](../README.md) — Quick start and overview
+- [Architecture](architecture.md) — How CodeGraph works internally
+- [Configuration](configuration.md) — All config options
+- [Storage Backends](storage-backends.md) — SQLite, LMDB, Redis, Postgres, MySQL deep-dive
+- [Semantic Search](semantic-search.md) — Embedding setup and hybrid search
\ No newline at end of file
diff --git a/docs/configuration.md b/docs/configuration.md
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@@ -0,0 +1,181 @@
+# Configuration Reference
+
+Complete reference for `.codegraph/config.toml`.
+
+## File Location
+
+```
+.codegraph/
+ config.toml # Main configuration
+ .gitignore # Pre-filled (index never committed)
+ version # Codegraph version that created the directory
+```
+
+## Full Configuration Example
+
+```toml
+# Language toggles (all 14 enabled by default)
+[languages]
+rust = true
+go = true
+python = true
+typescript = true
+javascript = true
+java = true
+c = true
+cpp = true
+csharp = true
+ruby = true
+php = true
+scala = true
+swift = true
+lua = true
+
+# C/C++ header handling
+# headers = "auto" # "auto" (default), "c", or "cpp"
+
+# Walker filters (gitignore syntax)
+[walker]
+include = ["**/*"]
+exclude = [
+ ".git/**",
+ ".codegraph/**",
+ "target/**",
+ "node_modules/**",
+ "*.min.js",
+ "*.lock"
+]
+
+# Storage backend
+[storage]
+type = "sqlite" # "sqlite" | "lmdb" | "redis" | "memory" | "postgres" | "mysql"
+# DSN override (optional; defaults derived from type)
+# dsn = "sqlite:///path/to/db.sqlite"
+# dsn = "lmdb:///path/to/db.lmdb"
+# dsn = "redis://localhost:6379"
+# For postgres/mysql: use dsns (shard list) + repo_id — see Storage Backends doc
+
+# Semantic search (vector KNN) — OFF by default
+[embedding]
+# backend = "fastembed" # "hashing"/unset = off
+# model = "bge-small-en-v1.5" # 384-dim, default
+# cache_dir = "~/.cache/codegraph/embeddings"
+# SQLite-only: HNSW ANN via sqlite-vss
+# vss_extension = "~/.cache/codegraph/embeddings/vss"
+# execution_provider = "coreml" # macOS hardware acceleration
+```
+
+---
+
+## Section Reference
+
+### `[languages]`
+
+Enable/disable individual language extractors. All 14 are enabled by default.
+
+| Key | Language | Tree-sitter Grammar |
+|-----|----------|---------------------|
+| `rust` | Rust | tree-sitter-rust |
+| `go` | Go | tree-sitter-go |
+| `python` | Python | tree-sitter-python |
+| `typescript` | TypeScript | tree-sitter-typescript |
+| `javascript` | JavaScript | tree-sitter-javascript |
+| `java` | Java | tree-sitter-java |
+| `c` | C | tree-sitter-c |
+| `cpp` | C++ | tree-sitter-cpp |
+| `csharp` | C# | tree-sitter-c-sharp |
+| `ruby` | Ruby | tree-sitter-ruby |
+| `php` | PHP | tree-sitter-php |
+| `scala` | Scala | tree-sitter-scala |
+| `swift` | Swift | tree-sitter-swift |
+| `lua` | Lua | tree-sitter-lua |
+
+**Headers**: The `headers` key controls `.h` file parsing:
+- `"auto"` (default): Detect from project — C++ if `.cpp`/`.hpp` present, C if `.c` present, inspect each `.h` for C++ syntax in mixed projects
+- `"c"`: Force all `.h` as C
+- `"cpp"`: Force all `.h` as C++
+
+### `[walker]`
+
+Controls which files are indexed. Uses `ignore::WalkBuilder` (same syntax as `.gitignore`).
+
+| Key | Type | Description |
+|-----|------|-------------|
+| `include` | `Vec` | Patterns to include (default `["**/*"]`) |
+| `exclude` | `Vec` | Patterns to exclude (default excludes `.git`, `.codegraph`, `target`, `node_modules`, `*.min.js`, `*.lock`) |
+
+**Note**: Walker filters apply *before* language detection. Excluded files are never parsed.
+
+### `[storage]`
+
+Selects the storage backend for the semantic graph.
+
+| `type` | Description | Default DSN | Notes |
+|--------|-------------|-------------|-------|
+| `sqlite` | SQLite WAL mode, single file | `sqlite:///.codegraph/db.sqlite` | Default, recommended for most uses |
+| `lmdb` | Memory-mapped KV, directory | `lmdb:///.codegraph/db.lmdb` | Mmap-friendly for large indexes |
+| `redis` | Redis backend | **Required** — no sensible default | Needs running Redis server |
+| `memory` | Ephemeral in-process | N/A | Nothing persisted; for testing |
+| `postgres` | PostgreSQL, sharded by `repo_id` | **Required** via `dsns` | Multi-tenant; see below |
+| `mysql` | MySQL, sharded by `repo_id` | **Required** via `dsns` | Multi-tenant; see below |
+
+**DSN override**: Set `dsn` to override the default for any backend.
+
+**Postgres/MySQL (multi-tenant, sharded)**:
+```toml
+[storage]
+type = "postgres" # or "mysql"
+dsns = [
+ "postgres://user:pass@db1:5432/codegraph",
+ "postgres://user:pass@db2:5432/codegraph",
+]
+# repo_id is auto-generated by `codegraph init` and written here
+# repo_id = 14028493579208694412
+```
+
+- Sharding: `shard = repo_id % len(dsns)`
+- Schema **not auto-applied** — run SQL files from `sql/postgres/` or `sql/mysql/` manually before indexing
+- See `sql/README.md` for full schema and sharding design
+
+### `[embedding]`
+
+Enables optional semantic search (vector KNN over symbol embeddings).
+
+| Key | Type | Default | Description |
+|-----|------|---------|-------------|
+| `backend` | `String` | unset (off) | `"fastembed"` to enable; `"hashing"` for deterministic fallback |
+| `model` | `String` | `"bge-small-en-v1.5"` | ONNX model name (384-dim) |
+| `cache_dir` | `String` | `"~/.cache/codegraph/embeddings"` | Global model cache directory |
+| `vss_extension` | `String` | unset | SQLite-only: path to sqlite-vss extension for HNSW ANN |
+| `execution_provider` | `String` | unset | `"coreml"` for macOS Apple Neural Engine/GPU |
+
+**Behavior**:
+- **Off by default** — no embedding model runs unless `backend = "fastembed"`
+- Release binary bundles fastembed (ONNX runtime) — no rebuild needed
+- With embeddings enabled, `codegraph_search_symbol` gains `match` modes: `"semantic"` (vector KNN) and `"hybrid"` (RRF merge of substring + semantic)
+- Vectors persisted with index — restarts reuse without re-embedding
+- **Error on load failure** — if model fails to load, opening index errors out (no silent fallback)
+
+**Pre-download model** (for offline indexing):
+```bash
+codegraph embed --model bge-small-en-v1.5
+```
+Requires binary built with `--features fastembed`.
+
+---
+
+## Environment Variable Overrides
+
+| Variable | Effect |
+|----------|--------|
+| `CODEGRAPH_CONFIG` | Path to config.toml (default: `.codegraph/config.toml`) |
+| `CODEGRAPH_INSTALL_DIR` | Install script target directory (default: `~/.local/bin`) |
+
+---
+
+## Related Docs
+
+- [Storage Backends](storage-backends.md) — Deep dive on each backend
+- [Semantic Search](semantic-search.md) — Embedding setup, models, sqlite-vss, CoreML
+- [Architecture](architecture.md) — How config maps to pipeline
+- [README](../README.md) — Quick start
\ No newline at end of file
diff --git a/docs/development.md b/docs/development.md
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--- /dev/null
+++ b/docs/development.md
@@ -0,0 +1,277 @@
+# Development Guide
+
+Building, testing, and contributing to CodeGraph.
+
+## Prerequisites
+
+- **Rust stable** ≥ 1.85 (edition 2024 used in `codegraph-graph`)
+- `cargo` (from rustup)
+- Optional: `clang` for some tree-sitter grammars (usually bundled)
+
+```bash
+# Verify toolchain
+rustc --version
+cargo --version
+```
+
+---
+
+## Quick Commands
+
+```bash
+# Build everything
+cargo build --workspace
+
+# Build release binary (what users get)
+cargo build --release -p codegraph
+
+# Run all tests
+cargo test --workspace
+
+# Lint (CI gate)
+cargo clippy --workspace --all-targets -- -D warnings
+
+# Format
+cargo fmt --all
+
+# Check all feature combinations
+cargo check --workspace --features sqlite
+cargo check -p codegraph-graph --features redis
+cargo check -p codegraph --features rdbms
+cargo check -p codegraph --features fastembed
+```
+
+---
+
+## Crate Overview
+
+```
+crates/
+ codegraph-core/ Error types + semgraph model (Symbol, Chain, CallRecord, markers)
+ codegraph-extract/ tree-sitter native + 14 LangSpec extractors + 5 hand-written
+ codegraph-graph/ GraphIndex: registry + 2 engines + pluggable storage + embeddings
+ codegraph-context/ Markdown/JSON context formatter
+ codegraph-api/ GraphApi wrapper on SharedGraphIndex (async queries)
+ codegraph-sboxes/ Behavior sandbox: Cranelift JIT + Rhai mock runtime
+ codegraph-mcp/ MCP server (rmcp SDK) + 24 tools + session management
+ codegraph-bench/ Benchmarks (criterion, codspeed, storage comparison)
+ codegraph/ CLI (init/deinit/embed/serve) + watcher (notify + debounce)
+```
+
+---
+
+## Per-Crate Test Commands
+
+```bash
+# Core model tests
+cargo test -p codegraph-core
+
+# Extraction: 30 tests (10 lib + 16 chains + 2 cpp + 2 extract)
+cargo test -p codegraph-extract
+
+# Graph: 60+ tests (search, storage, ingest, flow, reopen)
+cargo test -p codegraph-graph
+
+# API layer
+cargo test -p codegraph-api
+
+# MCP server + tools
+cargo test -p codegraph-mcp
+
+# Sandbox JIT: control flow + end-to-end traces
+cargo test -p codegraph-sboxes
+
+# Bench pipeline integration
+cargo test -p codegraph-bench
+
+# Installer
+cargo test -p codegraph-installer
+```
+
+---
+
+## Feature Flags
+
+### `codegraph-extract` (language support)
+
+| Feature | Languages |
+|---------|-----------|
+| `all-langs` (default) | All 14 |
+| `lang-rust` | Rust |
+| `lang-go` | Go |
+| `lang-python` | Python |
+| `lang-typescript` | TypeScript |
+| `lang-javascript` | JavaScript |
+| `lang-java` | Java |
+| `lang-c` | C |
+| `lang-cpp` | C++ |
+| `lang-csharp` | C# |
+| `lang-ruby` | Ruby |
+| `lang-php` | PHP |
+| `lang-scala` | Scala |
+| `lang-swift` | Swift |
+| `lang-lua` | Lua |
+
+```bash
+# Test single language
+cargo test -p codegraph-extract --features lang-python
+```
+
+### `codegraph-graph` (storage + features)
+
+| Feature | Description | Default on `codegraph` |
+|---------|-------------|------------------------|
+| `sqlite` | SQLite storage | ✅ |
+| `lmdb` | LMDB storage | ✅ |
+| `redis` | Redis storage (compile verify) | ❌ |
+| `postgres` | PostgreSQL storage | via `rdbms` |
+| `mysql` | MySQL storage | via `rdbms` |
+| `bloom-search` | Bloom filter for chain search | ✅ |
+| `fastembed` | ONNX embedding backend | ✅ (via codegraph-api) |
+| `apple-accel` | macOS CoreML for ONNX | ❌ (macOS only) |
+
+### `codegraph` binary
+
+| Feature | Description | Default |
+|---------|-------------|---------|
+| `rdbms` | Enable `postgres` + `mysql` | ✅ |
+| `fastembed` | Compile `codegraph embed` CLI | ❌ |
+| `apple-accel` | macOS CoreML | ❌ |
+
+### `codegraph-mcp` crate
+
+| Feature | Description | Default |
+|---------|-------------|---------|
+| `rdbms` | Enable `postgres` + `mysql` | ❌ |
+
+---
+
+## Important Notes
+
+### `codegraph-api` enables all `codegraph-graph` features
+
+```bash
+# This does NOT produce a slimmer binary — all storage drivers
+# and embedding backend are still compiled in via codegraph-api
+cargo build -p codegraph --no-default-features
+```
+
+To actually reduce binary size, you must build with minimal features on `codegraph-graph` AND avoid depending on `codegraph-api` (not practical for the main binary).
+
+### `apple-accel` is macOS-only
+
+```bash
+# Works
+cargo build --features fastembed,apple-accel --target x86_64-apple-darwin
+cargo build --features fastembed,apple-accel --target aarch64-apple-darwin
+
+# Fails
+cargo build --features fastembed,apple-accel --target x86_64-unknown-linux-gnu
+```
+
+---
+
+## Running Benchmarks
+
+```bash
+# Criterion benchmarks (statistical)
+cargo bench -p codegraph-bench
+
+# Single-pass measurement (JSON output)
+cargo run -p codegraph-bench -- --json
+
+# Storage backend comparison
+cargo run -p codegraph-bench -- --storage sqlite,lmdb,memory
+
+# CodSpeed (CI only — see .github/workflows/codspeed.yml)
+cargo codspeed build -p codegraph-bench --features codspeed
+```
+
+---
+
+## Release Process
+
+Handled by CI (`.github/workflows/release.yml`):
+
+1. Tag pushed: `vX.Y.Z`
+2. Builds for all targets:
+ - `x86_64-unknown-linux-musl`
+ - `aarch64-unknown-linux-gnu`
+ - `x86_64-apple-darwin`
+ - `aarch64-apple-darwin`
+ - `x86_64-pc-windows-msvc`
+3. Signs with cosign (keyless, GitHub OIDC)
+4. Attaches `.sig` + `.crt` to release
+5. Publishes to Homebrew tap, AUR, .deb/.rpm
+
+**Local release build**:
+```bash
+cargo build --release -p codegraph
+# Binary at target/release/codegraph
+```
+
+---
+
+## Project Structure
+
+```
+.
+├── crates/ # Workspace members
+├── docs/ # Documentation (this file + others)
+│ ├── architecture.md
+│ ├── comparison.md
+│ ├── configuration.md
+│ ├── development.md # This file
+│ ├── semantic-search.md
+│ ├── storage-backends.md
+│ ├── why-rust.md
+│ └── specs/ # Detailed spec docs
+├── scripts/ # Install scripts (sh/ps1)
+├── sql/ # Postgres/MySQL schemas
+├── packaging/ # .deb/.rpm packaging
+├── .github/workflows/ # CI/CD
+├── Cargo.toml # Workspace root
+└── README.md # Main entry point
+```
+
+---
+
+## Contributing
+
+1. Fork & branch
+2. `cargo fmt --all && cargo clippy --workspace --all-targets -- -D warnings`
+3. `cargo test --workspace`
+4. Add tests for new functionality
+5. Update relevant docs in `docs/`
+6. PR with clear description
+
+**Commit style**: Conventional commits (`feat:`, `fix:`, `docs:`, `refactor:`, `test:`)
+
+---
+
+## Debugging Tips
+
+```bash
+# Verbose logging
+RUST_LOG=codegraph=debug codegraph init
+
+# Specific crate
+RUST_LOG=codegraph_graph=trace codegraph init
+
+# MCP server debug
+RUST_LOG=codegraph_mcp=debug codegraph serve --mcp
+
+# Watcher debug
+RUST_LOG=codegraph=debug codegraph serve --mcp
+```
+
+---
+
+## Related Docs
+
+- [Architecture](architecture.md) — Pipeline and crate relationships
+- [Why Rust](why-rust.md) — Rewrite rationale and benchmarks
+- [Configuration](configuration.md) — Config reference
+- [Storage Backends](storage-backends.md) — Backend deep-dive
+- [Semantic Search](semantic-search.md) — Embedding setup
+- [README](../README.md) — Quick start
\ No newline at end of file
diff --git a/docs/semantic-search.md b/docs/semantic-search.md
new file mode 100644
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--- /dev/null
+++ b/docs/semantic-search.md
@@ -0,0 +1,157 @@
+# Semantic Search (Embeddings)
+
+Optional vector similarity search over symbol embeddings. Off by default.
+
+## Quick Start
+
+```toml
+# .codegraph/config.toml
+[embedding]
+backend = "fastembed"
+model = "bge-small-en-v1.5"
+cache_dir = "~/.cache/codegraph/embeddings"
+```
+
+```bash
+# Pre-download model (optional, for offline indexing)
+codegraph embed --model bge-small-en-v1.5
+
+# Re-index to generate embeddings
+codegraph init
+```
+
+## How It Works
+
+1. **Model**: BGE-small-en-v1.5 (384-dim, ONNX) via fastembed
+2. **Indexing**: Each symbol's name + signature → embedding vector
+3. **Storage**: Vectors persisted alongside graph (in same backend)
+4. **Query**: `codegraph_search_symbol` with `match = "semantic"` or `"hybrid"`
+5. **Hybrid**: Reciprocal Rank Fusion (RRF) merges substring + semantic results
+
+## Configuration Reference
+
+| Key | Required | Default | Description |
+|-----|----------|---------|-------------|
+| `backend` | Yes* | unset (off) | `"fastembed"` to enable; `"hashing"` for deterministic fallback |
+| `model` | No | `"bge-small-en-v1.5"` | ONNX model name (must be 384-dim) |
+| `cache_dir` | No | `"~/.cache/codegraph/embeddings"` | Global model cache |
+| `vss_extension` | No | unset | SQLite-only: path to sqlite-vss for HNSW ANN |
+| `execution_provider` | No | unset | `"coreml"` for macOS Apple Neural Engine/GPU |
+
+*Required to enable — if unset, semantic search is completely disabled (no model loads).
+
+## MCP Tool Changes
+
+With embeddings enabled, `codegraph_search_symbol` gains:
+
+| Match Mode | Description |
+|------------|-------------|
+| `contains` (default) | Substring match on lowercase names |
+| `prefix` / `suffix` / `exact` | String match variants |
+| `semantic` | Vector KNN — finds symbols by semantic similarity |
+| `hybrid` | RRF merge of `contains` + `semantic` |
+
+**Example**:
+```json
+// Semantic search
+{ "query": "user authentication", "match": "semantic", "limit": 10 }
+
+// Hybrid (recommended for best recall)
+{ "query": "auth user", "match": "hybrid", "limit": 10 }
+```
+
+## SQLite + sqlite-vss (HNSW ANN)
+
+For large indexes, exact KNN (brute-force) is slow. SQLite can use the `sqlite-vss` extension for HNSW approximate nearest neighbor.
+
+**Setup**:
+1. Install sqlite-vss (see https://github.com/asg017/sqlite-vss)
+2. Point `vss_extension` to the extension directory:
+```toml
+[embedding]
+backend = "fastembed"
+vss_extension = "~/.cache/codegraph/embeddings/vss"
+```
+3. Re-index — vectors will be indexed in HNSW
+
+**Trade-offs**:
+- HNSW: faster queries, approximate results, extra disk space
+- Brute-force: exact, slower on >100k vectors, no extra deps
+
+## macOS Hardware Acceleration (CoreML)
+
+On macOS, run embeddings on Apple Neural Engine / GPU via CoreML execution provider.
+
+**Build**:
+```bash
+cargo build --features fastembed,apple-accel
+```
+*Fails on non-macOS.*
+
+**Config**:
+```toml
+[embedding]
+backend = "fastembed"
+execution_provider = "coreml"
+```
+
+**Benefits**: 2–5× faster embedding inference on Apple Silicon.
+
+## Model Management
+
+**Pre-download** (offline indexing):
+```bash
+codegraph embed --model bge-small-en-v1.5 --cache-dir ~/.cache/codegraph/embeddings
+```
+- Requires binary built with `--features fastembed`
+- Downloads ONNX model to cache dir
+- Subsequent indexing works offline
+
+**Cache location**: `~/.cache/codegraph/embeddings/` (configurable via `cache_dir`)
+
+**Model files** (~50 MB):
+- `model.onnx` — the quantized BGE-small model
+- `tokenizer.json` — tokenizer config
+
+## Error Handling
+
+**Critical**: If the model fails to load (no network, missing ONNX runtime, corrupted cache), **opening the index errors out**. There is no silent fallback to lexical-only search.
+
+This is by design — silent fallback would return misleading results.
+
+**Troubleshooting**:
+- Verify `cache_dir` exists and is writable
+- Check ONNX Runtime is available (bundled in release binary)
+- Run `codegraph embed` to re-download model
+- Check logs: `RUST_LOG=codegraph_graph=debug codegraph init`
+
+## Performance
+
+| Metric | Value |
+|--------|-------|
+| Model size | ~50 MB (ONNX, int8 quantized) |
+| Dimensions | 384 |
+| Embedding latency | ~2–5 ms/symbol (CPU), ~0.5–1 ms (CoreML) |
+| Index overhead | 384 × 4 bytes × num_symbols (~1.5 KB/symbol) |
+| Query latency (brute-force) | O(N) — ~100k vectors = ~50 ms |
+| Query latency (HNSW) | O(log N) — ~100k vectors = ~2 ms |
+
+## When to Enable
+
+✅ **Enable if**:
+- Agents search by concept/intent ("error handling", "database connection")
+- Codebase has inconsistent naming (synonyms, abbreviations)
+- You want "fuzzy" symbol discovery
+
+❌ **Skip if**:
+- Strict name-based search is sufficient
+- Indexing speed is critical (embeddings add ~2–5 ms/symbol)
+- Disk space is constrained
+- Offline-only with no pre-download opportunity
+
+## Related Docs
+
+- [Configuration](configuration.md) — Full config.toml reference
+- [Storage Backends](storage-backends.md) — Vector storage per backend
+- [MCP Tools](../README.md#mcp-tools) — `codegraph_search_symbol` reference
+- [README](../README.md) — Quick start
\ No newline at end of file
diff --git a/docs/storage-backends.md b/docs/storage-backends.md
new file mode 100644
index 000000000..aa11ab486
--- /dev/null
+++ b/docs/storage-backends.md
@@ -0,0 +1,248 @@
+# Storage Backends
+
+Deep dive on CodeGraph's pluggable storage backends.
+
+## Overview
+
+CodeGraph's `GraphIndex` uses a pluggable storage abstraction. The backend is selected via `[storage] type` in `config.toml`.
+
+| Backend | Type | Persistence | Concurrency | Best For |
+|---------|------|-------------|-------------|----------|
+| SQLite | Embedded SQL | Single file (WAL) | Single-writer, multi-reader | Default, local projects |
+| LMDB | Embedded KV (mmap) | Directory | Multi-reader, single-writer | Large indexes, mmap-friendly |
+| Redis | Client-server | Remote | Multi-writer | Shared index, multi-process |
+| Memory | In-process | None | N/A | Testing, ephemeral |
+| PostgreSQL | Client-server (sharded) | Remote | Multi-writer | Multi-tenant, production |
+| MySQL | Client-server (sharded) | Remote | Multi-writer | Multi-tenant, production |
+
+---
+
+## SQLite (Default)
+
+**Config**:
+```toml
+[storage]
+type = "sqlite"
+# dsn = "sqlite:///absolute/path/to/db.sqlite" # optional override
+```
+
+**Characteristics**:
+- Single file: `.codegraph/db.sqlite` (WAL mode)
+- Entities + radix streams stored in tables
+- No external dependencies (bundled `rusqlite` with `bundled` feature)
+- WAL mode allows concurrent readers during write
+- **Default and recommended** for most local use
+
+**Performance** (from `crates/codegraph-bench/STORAGE_PERF.md` on `crates/` corpus):
+- Open + ingest (median): ~12–14 µs (in-memory baseline), ~40–43 ms (SQLite on disk)
+- On-disk size: ~590–690 KB for `crates/` workspace
+
+**Limitations**:
+- Single-writer — not suitable for concurrent multi-process writes
+- File-based — not network-accessible
+
+---
+
+## LMDB
+
+**Config**:
+```toml
+[storage]
+type = "lmdb"
+# dsn = "lmdb:///absolute/path/to/db.lmdb" # optional override
+```
+
+**Characteristics**:
+- Memory-mapped KV store (`.codegraph/db.lmdb/` directory)
+- Bundled C library (`lmdb-rkv`) — no system dependency
+- Zero-copy reads via mmap — excellent for read-heavy workloads
+- Single-writer, multi-reader (like SQLite)
+- **Smaller on-disk footprint** than SQLite (~2.2× smaller per benchmarks)
+
+**Performance** (same corpus):
+- Open + ingest (median): ~16–28 ms
+- On-disk size: ~270 KB for `crates/` workspace
+
+**When to choose**:
+- Very large indexes where mmap helps
+- Read-heavy workloads
+- You want smaller disk usage
+
+**Limitations**:
+- Single-writer
+- Directory-based (not a single file)
+- Map size must be configured for very large DBs (handled automatically)
+
+---
+
+## Redis
+
+**Config**:
+```toml
+[storage]
+type = "redis"
+dsn = "redis://localhost:6379" # REQUIRED
+```
+
+**Characteristics**:
+- Client-server — requires running Redis instance
+- Supports multi-process / multi-machine access
+- Uses Redis hashes/streams for entities and indexes
+- Connection pooling via `redis` crate with `tokio-comp`
+
+**When to choose**:
+- Multiple processes sharing one index
+- Index lives on a separate server
+- Need pub/sub for cache invalidation (future)
+
+**Limitations**:
+- Network latency on every operation
+- Requires Redis server management
+- No embedded mode
+
+---
+
+## Memory (Ephemeral)
+
+**Config**:
+```toml
+[storage]
+type = "memory"
+```
+
+**Characteristics**:
+- Pure in-process `DashMap` + in-memory engines
+- Nothing persisted — index lost on exit
+- Fastest for benchmarks/testing
+
+**When to choose**:
+- Unit tests
+- Ephemeral indexing (CI, scripting)
+- Benchmarking storage overhead
+
+---
+
+## PostgreSQL (Multi-Tenant, Sharded)
+
+**Config**:
+```toml
+[storage]
+type = "postgres"
+dsns = [
+ "postgres://user:pass@db1:5432/codegraph",
+ "postgres://user:pass@db2:5432/codegraph",
+]
+# repo_id auto-generated and written to config
+# repo_id = 14028493579208694412
+```
+
+**Architecture**:
+- Every table partitioned by leading `repo_id` (`u64`)
+- Each project root (`.codegraph/`) → its own `repo_id`
+- Sharding: `shard = repo_id % len(dsns)`
+- Re-indexing/deleting one repo never touches another
+
+**Schema** (manual apply required):
+```bash
+# Run against EVERY shard
+psql "$DSN" -f sql/postgres/001-initial-schema.sql
+psql "$DSN" -f sql/postgres/002-add-repos-registry.sql
+```
+
+**Tables** (per shard):
+- `repos` — registry of `repo_id` → root path
+- `entities` — symbols (partitioned by `repo_id`)
+- `chains` — call chains (partitioned)
+- `call_records` — resolved calls (partitioned)
+- `edges` — derived edges (partitioned)
+- `vectors` — embeddings (partitioned, if enabled)
+
+**Build**: Requires `rdbms` feature (on by default for `codegraph` binary):
+```bash
+cargo build --features rdbms
+cargo build -p codegraph-mcp --features rdbms
+```
+
+**When to choose**:
+- Multi-tenant SaaS (each customer = one repo_id)
+- Shared infrastructure, isolated data
+- Need SQL tooling for analytics
+
+**Limitations**:
+- Manual schema management
+- Network latency
+- More complex ops
+
+---
+
+## MySQL (Multi-Tenant, Sharded)
+
+**Config**:
+```toml
+[storage]
+type = "mysql"
+dsns = [
+ "mysql://user:pass@db1:3306/codegraph",
+ "mysql://user:pass@db2:3306/codegraph",
+]
+# repo_id auto-generated
+```
+
+**Schema** (manual apply):
+```bash
+mysql "$DB" < sql/mysql/001-initial-schema.sql
+mysql "$DB" < sql/mysql/002-add-repos-registry.sql
+```
+
+Same architecture as Postgres — partitioned by `repo_id`, sharded by `repo_id % N`.
+
+**When to choose**: Same as Postgres, but MySQL preferred.
+
+---
+
+## Backend Selection Guide
+
+| Scenario | Recommended |
+|----------|-------------|
+| Local development, single project | `sqlite` (default) |
+| Large local index, read-heavy | `lmdb` |
+| Multiple agents/processes same machine | `redis` or `lmdb` |
+| Team shared index (LAN) | `redis` |
+| Multi-tenant SaaS | `postgres` or `mysql` |
+| CI/testing | `memory` |
+| Production with SQL tooling needs | `postgres` |
+
+---
+
+## Switching Backends
+
+1. Update `config.toml` `[storage] type = "..."`
+2. Run `codegraph init` (or `codegraph_index` via MCP) — full re-index
+3. Old index files remain but are unused (safe to delete `.codegraph/db.*`)
+
+**Note**: No migration between backends — always full re-index from source.
+
+---
+
+## Performance Notes
+
+From `crates/codegraph-bench/STORAGE_PERF.md` (local `crates/` corpus, 3 runs median):
+
+| Backend | Open+Ingest | On-Disk Size | Query Latency (200 ops) |
+|---------|-------------|--------------|-------------------------|
+| `in_memory` | ~12 µs | N/A | ~84–90 ns/op |
+| `sqlite` | ~40–43 ms | ~590–690 KB | ~84–90 ns/op |
+| `lmdb` | ~16–28 ms | ~270 KB | ~84–90 ns/op |
+
+- Query latency dominated by in-memory engines (radix + chain search), not storage
+- High variance noted in SQLite/LMDB ingest ("measurement machine was loaded")
+- LMDB ~1.4–2.1× faster ingest than SQLite; ~2.2× smaller on disk
+
+---
+
+## Related Docs
+
+- [Configuration](configuration.md) — Full config.toml reference
+- [Architecture](architecture.md) — GraphIndex and storage abstraction
+- [SQL Schema](sql/README.md) — Postgres/MySQL schema details
+- [README](../README.md) — Quick start
\ No newline at end of file
diff --git a/docs/why-rust.md b/docs/why-rust.md
new file mode 100644
index 000000000..ae2e9b56b
--- /dev/null
+++ b/docs/why-rust.md
@@ -0,0 +1,132 @@
+# Why Rust? — The Rewrite Story
+
+CodeGraph is a from-scratch Rust rewrite of the previous TypeScript implementation.
+
+## The Old Stack (TypeScript)
+
+| Component | Technology | Pain Points |
+|-----------|------------|-------------|
+| Runtime | Node.js (embedded) | ~50 MB baseline, multi-second cold start |
+| Parsing | 20+ tree-sitter WASM grammars | WASM overhead, no parallel parsing |
+| Storage | Native SQLite addon (better-sqlite3) | Node-gyp builds, platform issues |
+| Distribution | Single binary via `pkg` | ~140 MB, not truly static |
+
+**Result**: ~140 MB binary, 2–3 second startup, complex build pipeline.
+
+---
+
+## The Rust Rewrite
+
+### What Changed
+
+| Before (TS) | After (Rust) | Impact |
+|-------------|--------------|--------|
+| Node runtime | **None** — static binary | -80 MB, sub-ms startup |
+| WASM grammars | **Statically-linked tree-sitter C** | Native speed, rayon parallelism |
+| Native SQLite addon | **Bundled `rusqlite` (bundled feature)** | No system deps, no node-gyp |
+| `pkg` bundler | **`cargo build --release` + `strip`** | Standard Rust toolchain |
+
+### Build Optimizations
+
+```toml
+# Cargo.toml (workspace)
+[profile.release]
+lto = "fat" # Cross-crate optimization
+codegen-units = 1 # Maximum optimization
+strip = true # Strip symbols
+panic = "abort" # Smaller binary, no unwinding
+```
+
+### Results
+
+| Metric | TypeScript | Rust | Improvement |
+|--------|------------|------|-------------|
+| Binary size | ~140 MB | **~58 MB** | **2.4× smaller** |
+| Cold start | ~2–3 s | **<100 ms** | **20–30× faster** |
+| Indexing (139 files) | ~1 s | **~190 ms** | **~5× faster** |
+| Memory (idle) | ~80 MB | **~15 MB** | **5× less** |
+| Dependencies | 500+ npm packages | **~100 crates** | Simpler supply chain |
+
+---
+
+## Why These Choices?
+
+### `tree-sitter` (C) over WASM
+
+- **Parallel parsing**: `rayon` thread pool across files — WASM can't do true parallelism
+- **Zero-copy**: Parse trees reference source bytes directly
+- **No WASM overhead**: Function calls, memory copies eliminated
+- **Grammar updates**: `tree-sitter` C libs updated independently
+
+### `rusqlite` (bundled SQLite) over native addon
+
+- **Pure Rust + bundled C**: `rusqlite` with `bundled` feature compiles SQLite from source
+- **No system SQLite needed**: Works on minimal containers (distroless, scratch)
+- **WAL mode**: Concurrent readers during write
+- **No node-gyp**: Eliminates entire class of build failures
+
+### Single Binary Philosophy
+
+```
+codegraph binary contains:
+ ├── tree-sitter parsers (14 languages, statically linked)
+ ├── SQLite (bundled, WAL mode)
+ ├── LMDB (bundled via lmdb-rkv)
+ ├── Redis client (async, tokio)
+ ├── Postgres/MySQL drivers (sqlx, compiled in)
+ ├── ONNX Runtime + fastembed (BGE-small model loader)
+ └── MCP server (rmcp SDK)
+```
+
+**No**:
+- External processes
+- Shared libraries (except libc)
+- Runtime downloads (model cached separately)
+- Daemon/background service
+
+---
+
+## Trade-offs
+
+| Gain | Cost |
+|------|------|
+| Fast startup | Longer compile time (~3–5 min clean) |
+| Small binary | Larger binary than minimal CLI (~58 MB) |
+| Parallel parsing | More complex build (C dependencies) |
+| No runtime deps | Can't hot-reload grammars (rebuild needed) |
+| Type safety | Learning curve for contributors |
+
+---
+
+## Verification
+
+```bash
+# Build release
+cargo build --release -p codegraph
+
+# Check size
+ls -lh target/release/codegraph
+# ~58 MB
+
+# Verify static linking
+ldd target/release/codegraph
+# Should show only libc, libdl, libpthread, libm, libgcc_s
+
+# Benchmark startup
+time target/release/codegraph --version
+# <100 ms
+
+# Benchmark indexing
+cd /path/to/project
+time target/release/codegraph init
+# ~190 ms for ~139 files
+```
+
+---
+
+## Related Docs
+
+- [Architecture](architecture.md) — Crate structure and pipeline
+- [Development](development.md) — Build, test, feature flags
+- [Configuration](configuration.md) — Storage/embedding backends
+- [README](../README.md) — Quick start
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