@lon-ask/dockit 0.1.0 → 0.1.2

package/README.md

@@ -1,496 +1,641 @@
 # Dockit
 
-Local documentation hub that aggregates multiple documentation source types (ZIP, Maven, Antora, AsciiDoc, GitHub Markdown) into a unified, searchable HTML bundle — useful as LLM context. Also supports **source code knowledge graphs** powered by Graphify (Tree-sitter AST), producing structural dependency graphs for 15+ languages.
+> Built with [OpenCode](https://opencode.ai) and [DeepSeek](https://deepseek.com)
 
-Ships with two search engines: a lightweight **TF-IDF engine** and a **hybrid semantic+keyword engine** (LanceDB + all-MiniLM-L6-v2 embeddings) configurable via a single toggle.
+> **Local documentation hub** — aggregate, index, and search your project's documentation and source code.
+> Runs entirely offline. Ships as a single CLI binary via npm.
 
-All operational data (SQLite DB, build outputs, search indexes, knowledge graphs, embeddings model cache) is stored in `~/.dockit/` by default. Override with the `DOCKIT_DATA_DIR` environment variable.
+## Why Dockit
 
-## Quick Start
+Modern software teams juggle multiple documentation sources: auto-generated API docs, hand-written Markdown guides, AsciiDoc references, Antora sites, Maven Javadoc JARs, ZIP archives. Each source lives in its own silo with its own search bar. When an LLM coding agent needs to answer a framework question, it either hallucinates from training data or scrolls through GitHub.
+
+Dockit solves this by ingesting **six documentation source types** and **source code** into a single, offline searchable index. It runs entirely on your machine — no cloud, no API keys, no internet required after the initial build.
+
+### What it does
+
+- **Indexes documentation** from ZIP bundles, Maven Javadoc, Antora sites, AsciiDoc repos, GitHub Markdown repos
+- **Builds source code knowledge graphs** via Graphify (Tree-sitter AST) — traces imports, calls, and inheritance across 15+ languages
+- **Searches with hybrid TF-IDF + vector semantic engine** — keyword precision + conceptual understanding
+- **Exposes an MCP server** so AI coding agents (Claude, Cline, OpenCode) can query docs on-demand
+- **Works completely offline** — LanceDB embedded vector DB, ONNX embeddings model, local SQLite
+
+### Who it's for
+
+| Role | Use case |
+|------|----------|
+| **LLM coding agents** | Query up-to-date framework docs instead of relying on stale training data |
+| **Developers** | Search your project's docs + code structure from the terminal |
+| **Teams** | Pre-build doc indexes once, share across the team |
+| **Air-gapped environments** | Full offline operation with pre-seeded models and indexes |
+
+---
+
+## Installation
+
+### Method 1: npm registry (recommended)
+
+```bash
+npm install -g @lon-ask/dockit
+```
+
+After global install, the `dockit` command is available in your PATH:
+
+```bash
+dockit --help
+dockit list
+```
+
+### Method 2: npx (zero-install)
+
+Run dockit on-demand without installing anything:
 
 ```bash
-# 1. Clone and install
-git clone https://github.com/your-org/dockit.git
+npx @lon-ask/dockit list
+npx @lon-ask/dockit init --path ./my-project --code-path src
+npx @lon-ask/dockit search my-project "authentication"
+```
+
+`npx` downloads the package to a temp cache and executes it. Perfect for one-off usage or CI pipelines. Set `DOCKIT_DATA_DIR` to persist data across invocations.
+
+### Method 3: Build from source
+
+```bash
+git clone https://github.com/karthik20/dockit.git
 cd dockit
 npm install
-pip3 install graphify openai   # optional — for source code graphs
+npm run build
+npm link                    # makes 'dockit' available globally
+
+pip3 install graphify        # optional — for source code knowledge graphs
+```
+
+### Prerequisites
 
-# 2. Make CLI available globally
-npm link
+| Requirement | Needed for |
+|-------------|-----------|
+| Node.js 18+ | Runtime |
+| Python 3.8+ & pip | Graphify source code graphs (optional) |
+| Graphify (`pip install graphify`) | `source-code` source type, `graphifyEnabled` on doc sources |
+| Maven (`mvn`) | Maven Javadoc source type |
+| Antora CLI | Antora source type (auto-installed via npm dep) |
+| Git | Cloning repos for AsciiDoc, Markdown, Source Code sources |
 
-# 3a. Build pre-configured docs (one-time per entry)
-dockit build quarkus
+### Data storage
 
-# 3b. Or init a project with source code + markdown scanning
-dockit init --path /path/to/project --code-path src
+All operational data lives in `~/.dockit/` by default. Override with `DOCKIT_DATA_DIR`:
 
-# 4. Start searching
-dockit search quarkus "configure cache"
-dockit graph query dockit "BuildUseCase"   # if source-code built
+```bash
+export DOCKIT_DATA_DIR=/path/to/custom/data
 ```
 
-## Pre-configured Documentation
+| Path | Contents |
+|------|----------|
+| `~/.dockit/dockit.db` | SQLite database (entries, sources, builds) |
+| `~/.dockit/dockit.yaml` | Your config (auto-created by `dockit init`) |
+| `~/.dockit/.lancedb/` | Vector search index (LanceDB) |
+| `~/.dockit/models/` | ONNX embedding model cache |
+| `~/.dockit/{entryId}/bundle/` | Built HTML docs per entry |
+| `~/.dockit/{entryId}/graph.json` | Knowledge graph (source-code entries) |
 
-| Entry | Version | Source Type | Description |
-|-------|---------|-------------|-------------|
-| **Quarkus** | 3.35 | AsciiDoc | Quarkus framework documentation |
-| **Quarkus Core** | 3.35.2 | Maven Javadoc | Quarkus Core API reference |
-| **React** | 19 | GitHub Markdown | React library documentation |
-| **Spring Boot** | 3.5.x | Antora | Production-ready Spring applications |
-| **Spring Framework** | 7.x | Antora | Core Spring ecosystem reference |
-| **Quarkus Source Code** | 3.35 | Source Code | Quarkus framework source — knowledge graph |
-| **Quarkus (Docs + Code)** | 3.35 | AsciiDoc + Source Code | Docs + code graph combined |
-| **Dockit** | 1.0 | Source Code + Markdown | Self-hosted dockit project entry |
+---
 
-Add your own entries by editing `dockit.yaml` or using `dockit init` — see [Supported Sources](#supported-documentation-sources) below.
+## Quick Start
 
-## Search Engine
+### Index your own project (30 seconds)
 
-Dockit ships two search engines toggleable via `dockit.yaml`:
+```bash
+# From your project directory
+npx @lon-ask/dockit init --code-path src
+
+# This:
+#   1. Scans all .md files → searchable docs
+#   2. Runs Graphify on src/ → knowledge graph
+#   3. Builds vector search index
+#   4. Saves config to ~/.dockit/dockit.yaml
+```
 
-```yaml
-search:
-  engine: vector    # 'vector' (default) | 'json' (TF-IDF fallback)
+Now search:
+
+```bash
+npx @lon-ask/dockit search my-project "authentication"
+npx @lon-ask/dockit graph gods my-project
+npx @lon-ask/dockit graph path my-project "createApp" "startServer"
 ```
 
-| | JSON (TF-IDF) | Vector (Hybrid) |
-|---|---|---|
-| **Storage per entry** | ~300 KB | ~32 MB (LanceDB) |
-| **Runtime memory** | Minimal | ~200 MB |
-| **Build time** | Fast | Slower (embeds docs via ONNX) |
-| **Search method** | Term-frequency scoring (title 10x, headings 3x, body 1x) | Hybrid: parallel cosine ANN + BM25 FTS → RRF fusion |
-| **Keyword precision** | High (exact term matches) | Very high (FTS component recovers keywords) |
-| **Semantic matching** | None | Yes (finds conceptually related docs even without exact terms) |
-| **Model** | None | `all-MiniLM-L6-v2` via `@huggingface/transformers` (~88 MB ONNX) |
-| **Works offline** | Yes — zero dependencies | Yes — model bundles in npm package |
+### Index framework docs
 
-### How hybrid search works
+```bash
+# Build pre-configured entries from dockit.yaml
+dockit build quarkus          # 30 min, 3500+ AsciiDoc pages → ~800 MB vector index
+dockit build react            # 2 min, 200+ Markdown pages
+dockit build spring-boot      # 15 min, Antora site
 
-```
-query → vector (cosine ANN) + BM25 (FTS) in parallel
-         → deduplicate per-path → RRF fusion → top N
+# Search across all built entries
+dockit search "configure cache"
 ```
 
-- Vector search finds semantically related pages (e.g., "Ahead-of-Time Caching" for a cache query)
-- FTS recovers exact keyword matches (e.g., "caffeine" in the Caching guide)
-- Reciprocal Rank Fusion combines both with dynamic weighting: confident FTS gets 2x weight, uncertain FTS gets 0.7x
-- Title matches in FTS results get an additional 1.5x boost
+### Use with an AI agent
 
-### When to use each
+Add dockit as an MCP server in your AI tool's config:
 
-- **`json`**: Low-resource environments, fast builds, or when exact keyword matching is sufficient
-- **`vector`** (default): Better discovery of non-obvious matches, section-level chunking with heading context in results, hybrid search that matches both keywords and concepts
+```json
+// ~/.config/opencode/opencode.json
+{
+  "mcp": {
+    "dockit": {
+      "type": "local",
+      "command": ["npx", "@lon-ask/dockit", "mcp"],
+      "enabled": true
+    }
+  }
+}
+```
 
-## CLI Usage (Recommended)
+The agent can then call `dockit_search`, `dockit_graph_query`, etc. automatically.
 
-The CLI is the primary way to interact with Dockit. Works from any directory, requires no server process, and is ideal for LLM agents that can execute shell commands.
+---
 
-### Commands
+## CLI Commands
 
 | Command | Description |
 |---------|-------------|
+| `dockit init --path <dir> [--code-path <sub>]` | Index a local project (markdown + source code) |
 | `dockit search [<entry>] <query>` | Search documentation |
-| `dockit search <query>` | Global search — top result per entry |
-| `dockit search [<entry>] <query> --get-top [N]` | Fetch full content for top N results (default 3) |
+| `dockit search [<entry>] <query> --get-top [N]` | Search + fetch full content for top N results |
 | `dockit list` | List all entries |
-| `dockit build <entry>` | Build documentation for an entry |
+| `dockit build <entry>` | Build/rebuild documentation for an entry |
 | `dockit status <entry>` | Check build status |
-| `dockit get <entry> <path>` | Fetch full document content |
-| `dockit graph query <entry> <query>` | Search knowledge graph nodes by name, file, or type |
-| `dockit graph path <entry> <from> <to>` | Find shortest dependency path between two nodes |
-| `dockit graph gods <entry>` | List most connected (god) nodes |
-| `dockit graph explain <entry> <node>` | Show node details and connections |
-| `dockit init --path <dir> [--code-path <subdir>]` | Initialize a project as a dockit source |
-| `dockit dev` | Start dev servers (web UI) |
-| `dockit serve` | Start production server |
-| `dockit mcp` | Start MCP server |
+| `dockit get <entry> <path>` | Fetch full document by path |
+| `dockit graph query <entry> <query>` | Search knowledge graph nodes |
+| `dockit graph path <entry> <from> <to>` | Find shortest dependency path |
+| `dockit graph gods <entry>` | List most-connected nodes |
+| `dockit graph explain <entry> <node>` | Show node details + connections |
+| `dockit dev` | Start dev servers (Web UI on :5173 + API on :3001) |
+| `dockit serve [--port <p>]` | Start production REST server |
+| `dockit mcp` | Start MCP server for AI agents |
 
-### Search Workflow
+### Flags
+
+| Flag | Applies to | Description |
+|------|-----------|-------------|
+| `--json` | search, list, status, graph | Output as JSON |
+| `--limit <n>` | search, graph query, graph gods | Max results |
+| `--get-top [N]` | search | Fetch full content for top N (default 3) |
+| `--name <n>` | init | Entry display name |
+| `--version <v>` | init | Entry version string |
+| `--code-path <p>` | init | Subdirectory for source code scanning |
+| `--port <p>` | serve, mcp --http | Custom port |
 
-**Step 1: Global search** — discover which entries are relevant
+### Search workflow
 
 ```bash
+# Step 1: Discover relevant entries
 dockit search "cache"
-# Returns top result per entry:
-#   [React] cache
-#   [Quarkus] caching-guide
-#   [Quarkus Core] Cache API
+# → [React] cache  [Quarkus] caching-guide  [Quarkus Core] Cache API
+
+# Step 2: Deep-dive into one entry with full content
+dockit search quarkus "cache" --get-top 3
+# → Returns plain text of top 3 matching documents
+
+# Step 3: JSON output for scripts
+dockit search react "useState" --get-top 3 --json
 ```
 
-**Step 2: Scoped search** — dive deeper into the chosen entry
+### Knowledge graph workflow
 
 ```bash
-dockit search quarkus "cache" --get-top 3
-# Returns full content for top 3 Quarkus cache documents
+# Find nodes matching a term
+dockit graph query my-project "database" --limit 5
+
+# See the most-connected nodes (entry points, god classes)
+dockit graph gods my-project
+
+# Trace how two modules are connected
+dockit graph path my-project "app.ts" "database.ts"
+
+# Inspect a node's connections
+dockit graph explain my-project "createApp"
 ```
 
-### Knowledge Graph Queries
+---
 
-For `source-code` entries built with Graphify:
+## Supported Documentation Sources
 
-```bash
-# Search nodes
-dockit graph query dockit-code "BuildUseCase"
+| Type | What it indexes | Remote | Local |
+|------|----------------|--------|-------|
+| **GitHub Markdown** | All `.md` files in a repo | `repoUrl`, `sourcePath`, `branch` | `localPath` |
+| **AsciiDoc** | `.adoc` files via Asciidoctor | `repoUrl`, `sourcePath` | `localPath`, `zipPath` |
+| **Antora** | Multi-page Antora documentation sites | `repoUrl` | `localPath`, `zipPath` |
+| **ZIP Bundle** | Pre-built HTML in a ZIP archive | `url` | `localPath` |
+| **Maven Javadoc** | Javadoc JAR from Maven Central | — | `localJar`, `useMavenCommand` |
+| **Source Code** | Knowledge graph via Graphify Tree-sitter AST | `repoUrl`, `sourcePath`, `branch` | `localPath` |
 
-# List most connected nodes
-dockit graph gods dockit-code --limit 5
+### Source code knowledge graphs
+
+The `source-code` source type runs [Graphify](https://github.com/safishamsi/graphify) which parses your code with Tree-sitter (AST) and produces a `graph.json` containing nodes (classes, functions, files) and edges (imports, calls, inherits). No LLM required — pure static analysis. Supports TypeScript, JavaScript, Python, Java, Go, Rust, C++, and 10 more languages.
 
-# Find shortest path between two nodes
-dockit graph path dockit-code "BuildUseCase" "SourceCodeSourceProcessor"
+Add `graphifyEnabled: true` to any doc source to also generate a graph alongside the docs:
 
-# Show node details and connections
-dockit graph explain dockit-code "BuildUseCase"
+```yaml
+sources:
+  - type: github-markdown
+    label: "API Docs"
+    repoUrl: "https://github.com/myorg/myrepo.git"
+    sourcePath: "docs"              # where .md files live
+    graphifyEnabled: true
+    graphifySourcePath: "src"       # where source code lives
 ```
 
-### Init a Project
+---
 
-```bash
-# From project root — auto-detects name
-dockit init --code-path apps
+## Search Engine
 
-# With explicit path and version
-dockit init --path /path/to/project --name "MyApp" --version "2.0" --code-path src
+Dockit ships two engines, toggled via `dockit.yaml`:
 
-# This creates:
-#   - source-code source (graphify on --code-path)
-#   - github-markdown source (scans all .md files)
-#   - Builds both immediately
+```yaml
+search:
+  engine: vector    # 'vector' (default) | 'json' (TF-IDF)
 ```
 
-### Flags
-
-| Flag | Description |
-|------|-------------|
-| `--json` | Output as JSON (for search, list, status, graph) |
-| `--limit <n>` | Max results (default 20) |
-| `--get-top [N]` | Fetch full content for top N results (default 3) |
-| `--port <port>` | Custom port (for serve, mcp --http) |
+| | JSON (TF-IDF) | Vector (Hybrid) |
+|---|---|---|
+| **Storage** | ~300 KB per entry | ~32 MB per entry |
+| **Memory** | Minimal | ~200 MB |
+| **Build speed** | Fast | Slower (embeds all documents) |
+| **Keyword match** | Exact term frequency | BM25 FTS (very high precision) |
+| **Semantic match** | None | Yes (cosine ANN via all-MiniLM-L6-v2) |
+| **Model** | None | 88 MB ONNX, bundled in package |
+| **Offline** | Yes | Yes |
 
-### Examples
+### How hybrid search works
 
-```bash
-# Global search — see which entries match
-dockit search "hooks"
+```
+query → [vector cosine ANN] + [BM25 full-text search] in parallel
+         → deduplicate per document path
+         → Reciprocal Rank Fusion combining both
+         → dynamic FTS weighting: 2x for confident matches, 0.7x for uncertain
+         → title match bonus: 1.5x when query terms appear in headings
+```
 
-# Scoped search with full content
-dockit search react "how to create a hook" --get-top
+---
 
-# JSON output for scripts/agents
-dockit search react "useState" --get-top 3 --json
+## Config File (`dockit.yaml`)
 
-# Build documentation
-dockit build quarkus
-dockit status quarkus
+After running `dockit init`, your config is at `~/.dockit/dockit.yaml`:
 
-# Fetch a specific document
-dockit get react react-docs-markdown/reference/react/hooks.html
+```yaml
+entries:
+  - id: my-project
+    name: My Project
+    version: "1.0"
+    description: My project source code and documentation
+    sources:
+      - type: source-code
+        label: "my-project Code"
+        localPath: /home/user/projects/my-project
+        sourcePath: src
+      - type: github-markdown
+        label: "my-project Markdown"
+        localPath: /home/user/projects/my-project
 
-# Graph queries
-dockit graph query dockit-code "SourceCodeSourceProcessor"
-dockit graph gods dockit-code
+search:
+  engine: vector
 ```
 
-## MCP Server (Optional)
+Config resolution order:
+1. `~/.dockit/dockit.yaml` — user home (created by `dockit init`)
+2. `./dockit.yaml` — project root (development/backward compatibility)
+
+---
+
+## LLM Integration
+
+Dockit is designed to be an **on-demand knowledge source for AI coding agents**. Instead of relying on stale training data or hallucinated API references, LLMs can query dockit at runtime for up-to-date, project-specific documentation and source code structure.
+
+### How it works
+
+Dockit ships with a **skill file** (`SKILL.md`) that teaches LLMs how to use the tool. When an LLM coding agent has access to dockit (via CLI, MCP, or shell commands), it follows this workflow:
 
-Dockit exposes an MCP (Model Context Protocol) server for AI tools like Claude Desktop, Cline, and OpenCode.
+```
+User question → dockit search "query"      → discover relevant entries
+              → dockit search <entry> "query" --get-top  → retrieve full docs
+              → dockit graph query <entry> "node"        → trace code structure
+              → Answer user with retrieved content as context
+```
+
+The skill file instructs the LLM to:
+- Strip conversational filler from queries (keep only technical terms)
+- Always scope searches to the right entry once identified
+- Prefer dockit documentation over training data
+- Use knowledge graph queries for source-code entries
+- Show attribution (source type, repo, version) with answers
 
 ### OpenCode
 
+OpenCode supports multiple integration modes:
+
+**Skill mode** (recommended) — OpenCode reads `SKILL.md` automatically from the skill registry:
+
+```bash
+# When dockit is configured as a skill in ~/.config/opencode/skills/dockit/
+# OpenCode loads SKILL.md instructions and invokes dockit CLI commands directly
+opencode> "How do I configure cache in Quarkus?"
+# OpenCode runs: dockit search quarkus "configure cache" --get-top
+```
+
+**MCP mode** — dockit exposes as an MCP server for structured tool calls:
+
 ```json
-// ~/.config/opencode/opencode.json
 {
   "$schema": "https://opencode.ai/config.json",
   "mcp": {
     "dockit": {
       "type": "local",
-      "command": ["bash", "/path/to/dockit/scripts/mcp-wrapper.sh"],
+      "command": ["npx", "@lon-ask/dockit", "mcp"],
       "enabled": true
     }
   }
 }
 ```
 
-### Claude Desktop / Cline
+**CLI mode** — dockit commands are shell commands the agent can execute:
+
+```bash
+dockit search react "useState" --get-top 3 --json
+```
+
+### Claude Code
+
+Add dockit as an MCP server in Claude Code's config:
 
 ```json
-// ~/.claude/claude_desktop_config.json
 {
   "mcpServers": {
     "dockit": {
-      "command": "bash",
-      "args": ["/path/to/dockit/scripts/mcp-wrapper.sh"]
+      "command": "npx",
+      "args": ["@lon-ask/dockit", "mcp"]
     }
   }
 }
 ```
 
-### HTTP Transport
+Claude can then call `dockit_search`, `dockit_get_doc`, `dockit_graph_query`, and all other MCP tools directly. The skill instructions in `SKILL.md` guide it to use the right tool for each query type.
 
-```bash
-# Start HTTP bridge on port 3456
-DOCKIT_MCP_HTTP_PORT=3456 ./scripts/mcp-wrapper.sh
+**Claude Code with CLI fallback** — if MCP is unavailable, Claude can run dockit as a shell command:
 
-# Then curl:
-curl -X POST http://localhost:3456 \
-  -H "Content-Type: application/json" \
-  -d '{"jsonrpc":"2.0","id":1,"method":"tools/list","params":{}}'
+```bash
+npx @lon-ask/dockit search quarkus "reactive routes" --get-top 3 --json
 ```
 
-### MCP Tools
-
-| Tool | Description |
-|------|-------------|
-| `dockit_list_entries` | List all configured entries |
-| `dockit_find_entry` | Find entries by name/description |
-| `dockit_search` | Search within a specific entry |
-| `dockit_global_search` | Search across all entries |
-| `dockit_get_doc` | Fetch full document content |
-| `dockit_build` / `dockit_build_status` | Build / check status |
-| `dockit_graph_query` | Search knowledge graph (MCP only) |
-| `dockit_graph_path` | Find shortest path between nodes (MCP only) |
-| `dockit_graph_explain` | Node details with edges (MCP only) |
-| `dockit_graph_gods` | Most connected nodes (MCP only) |
-
-## How LLMs Use Dockit
-
-Dockit includes `SKILL.md` — a skill file that instructs LLMs how to use Dockit effectively. When an LLM has access to the `dockit` CLI or MCP tools, it follows this workflow:
-
-1. **`dockit list`** / **`dockit_list_entries`** — discover available documentation
-2. **`dockit search "query"`** — global search to find relevant entries
-3. **`dockit search <entry> "query" --get-top`** — scoped search with full content
-4. **For source-code entries**: use `dockit graph query <entry> "node"` for structural queries
-5. **Answer the user's question** using the retrieved documentation as context
-
-The LLM strips conversational filler from queries, scopes searches to the right entry, and prefers Dockit documentation over training data.
-
-## Supported Documentation Sources
-
-| Type | Description | Remote Fields | Local/Offline Fields |
-|------|-------------|---------------|---------------------|
-| **ZIP Bundle** | Download or extract a ZIP of HTML documentation | `url` | `localPath` — path to pre-downloaded .zip |
-| **Maven Artifact** | Download a documentation JAR (javadoc) from Maven Central | *(none extra)* | `useMavenCommand: true` — uses local Maven + settings.xml; `localJar` — path to pre-downloaded .jar |
-| **Antora** | Build a multi-page HTML site with Antora | `repoUrl` | `localPath` — path to pre-cloned repo |
-| **AsciiDoc** | Convert `.adoc` files to HTML | `repoUrl`, `sourcePath` (optional) | `localPath` — path to pre-cloned repo |
-| **GitHub Markdown** | Clone a GitHub repo and convert `.md` files to HTML | `repoUrl`, `sourcePath` (optional), `branch` (optional) | `localPath` — path to pre-cloned repo |
-| **Source Code** | Build a knowledge graph via Graphify (Tree-sitter AST) | `repoUrl`, `sourcePath` (optional), `branch` (optional) | `localPath` — path to local repo |
-| **Combined** | Add `graphifyEnabled: true` on doc sources (AsciiDoc, Markdown, Antora) to also generate a graph | *(inherits from parent type)* | *(inherits from parent type)* |
-
-### Source code knowledge graphs
-
-The `source-code` source type runs [Graphify](https://github.com/anomalyco/graphify) (Tree-sitter AST parser) on the source directory, producing a `graph.json` with nodes (classes, functions, files) and edges (imports, calls, inherits). Supports 15+ languages including TypeScript, JavaScript, Python, Java, Go, Rust, and C++.
-
-**Configuration fields:**
+### Cline (VS Code)
 
-| Field | Description |
-|-------|-------------|
-| `repoUrl` / `localPath` / `zipPath` | Source acquisition (same pattern as other types) |
-| `sourcePath` | Subdirectory to scan for code files |
-| `graphifySourcePath` | Separate subdirectory for graphify (when different from sourcePath e.g. docs vs code) |
-
-For existing doc sources (AsciiDoc, GitHub Markdown, Antora) that point to a repo containing source code, toggle `graphifyEnabled: true` and set `graphifySourcePath` to scan the code during build:
-
-```yaml
-sources:
-  - type: asciidoc
-    label: "Docs"
-    repoUrl: "https://github.com/myorg/myrepo.git"
-    sourcePath: "docs"           # doc files
-    graphifyEnabled: true
-    graphifySourcePath: "src"    # code files for graph
+```json
+{
+  "mcpServers": {
+    "dockit": {
+      "command": "npx",
+      "args": ["@lon-ask/dockit", "mcp"]
+    }
+  }
+}
 ```
 
-## Offline / Proxy Mode
+### General LLM Integration
 
-For environments behind corporate proxies or without internet access, Dockit supports multiple fallback mechanisms:
+Any LLM that can execute shell commands or make HTTP requests can use dockit:
 
-### Source Repositories (local clones)
+**Via CLI (shell access)**:
+```bash
+# Build an entry
+npx @lon-ask/dockit build react
+# Search with full content
+npx @lon-ask/dockit search react "hooks" --get-top 3 --json
+# Query knowledge graph
+npx @lon-ask/dockit graph gods my-project --json
+```
 
-Each source type supports local paths that take precedence over remote URLs:
+**Via REST API** (when server is running):
+```bash
+dockit serve --port 3001 &
+curl "http://localhost:3001/api/entries/react/search?q=hooks"
+curl "http://localhost:3001/api/graph/my-project/query?q=database"
+```
 
-```yaml
-# dockit.yaml — local mode entries
-entries:
-  - id: quarkus-local
-    name: Quarkus (Local)
-    version: "3.35"
-    sources:
-      - type: asciidoc
-        label: "Quarkus Docs"
-        localPath: "/home/user/repos/quarkus"
-        sourcePath: "docs/src/main/asciidoc"
+**Via HTTP MCP bridge**:
+```bash
+DOCKIT_MCP_HTTP_PORT=3456 npx @lon-ask/dockit mcp --http &
+curl -X POST http://localhost:3456 \
+  -H "Content-Type: application/json" \
+  -d '{"jsonrpc":"2.0","id":1,"method":"tools/call","params":{"name":"dockit_search","arguments":{"entry":"react","query":"hooks"}}}'
 ```
 
-### Embedding Model (air-gapped vector search)
+### Skills Registry
+
+Dockit's `SKILL.md` is also registered as a skill file. When placed in an LLM agent's skill directory, it provides:
 
-The embedding model downloads on first `embed()` call by default into `~/.dockit/models/`. Override with `DOCKIT_DATA_DIR` or `configure({ cacheDir: '...' })`. For air-gapped environments:
+1. **Tool instructions** — which commands to use and when
+2. **Query refinement rules** — stripping filler, keeping technical terms
+3. **Workflow patterns** — discover → search → retrieve → graph
+4. **Attribution rules** — always cite source type, repo, version
 
-**Option A — Pre-seed on connected machine, then copy:**
+To register dockit as a skill:
 ```bash
-# On connected machine
-npm run download-model -w packages/embeddings
+# For OpenCode
+cp SKILL.md ~/.config/opencode/skills/dockit/SKILL.md
 
-# Copy ~/.dockit/models/ to the target machine
+# For other agents that support skill files, place SKILL.md in their skills directory
 ```
 
-**Option B — Install offline via npm:**
-The model ONNX bundle ships inside the `@dockit/embeddings` npm package under `packages/embeddings/model/`. If `~/.dockit/models/` is empty at first `embed()` call, it will attempt to download — set `DOCKIT_DATA_DIR` to point to a pre-seeded directory or use `configure({ cacheDir: '/path/to/model' })`.
+### MCP Tools Reference
 
-### Pre-built Index Bundling
+| Tool | Description |
+|------|-------------|
+| `dockit_list_entries` | List all configured entries |
+| `dockit_find_entry` | Find entries by name/description |
+| `dockit_search` | Search within a specific entry |
+| `dockit_global_search` | Search across all entries |
+| `dockit_get_doc` | Fetch full document content |
+| `dockit_build` | Build documentation for an entry |
+| `dockit_build_status` | Check build status |
+| `dockit_graph_query` | Search knowledge graph nodes |
+| `dockit_graph_path` | Find dependency path between two nodes |
+| `dockit_graph_explain` | Show node details and connections |
+| `dockit_graph_gods` | List most-connected (god) nodes |
 
-For environments where even building is impractical, LanceDB and JSON indexes can be pre-built and bundled:
+---
 
-1. Build indexes on a connected machine:
-   ```bash
-   dockit build quarkus
-   dockit build spring-boot
-   # ... all desired entries
-   ```
-2. Package the `~/.dockit/` directory (or specific `.lancedb/` + `index.json` files)
-3. Deploy to target machines via the same `~/.dockit/` path
+## Web UI
 
-### Proxy Configuration
+Dockit includes a React-based graphical interface for managing entries, configuring sources, and browsing documentation. It runs alongside the API server.
 
-Standard proxy environment variables:
+### Starting the UI
 
 ```bash
-export HTTP_PROXY=http://proxy.corp:8080
-export HTTPS_PROXY=http://proxy.corp:8080
-```
-
-Or override the HuggingFace CDN host via code:
+# Development mode — starts both API server + Vite dev UI concurrently
+npx @lon-ask/dockit dev
+# API → http://localhost:3001
+# UI  → http://localhost:5173
 
-```ts
-import { env } from '@huggingface/transformers';
-env.remoteHost = 'https://internal-mirror.corp';  // point to internal mirror
+# Production mode — API server only (UI not served yet)
+npx @lon-ask/dockit serve --port 3001
 ```
 
-### Native Binaries
+> **Note**: The first `npx` run downloads `tsx` and `vite` (if not locally cached). Subsequent runs use the cached versions and start within seconds.
 
-`@lancedb/lancedb` ships prebuilt binaries for linux x64/arm64, macOS x64/arm64, and Windows x64/arm64 — no compilation needed.
+### How it works under the hood
 
-### Additional offline fields
+`dockit dev` spawns two processes in parallel:
+- **API server** — `npx tsx watch apps/server/src/index.ts` (Express + TypeScript, hot reload)
+- **Web UI** — `npx vite apps/client` (React dev server with HMR, port 5173)
 
-| Source Type | Fields (all take precedence over remote) |
-|-------------|------------------------------------------|
-| **ZIP** | `localPath` — path to pre-downloaded .zip |
-| **Maven** | `useMavenCommand: true` — uses local `~/.m2/settings.xml` (proxies, mirrors); `localJar` — pre-downloaded .jar |
-| **Antora** | `localPath` — pre-cloned repo |
-| **AsciiDoc** | `localPath` — pre-cloned repo (kept, not cleaned up) |
-| **GitHub Markdown** | `localPath` — pre-cloned repo |
-| **Source Code** | `localPath` — local repo directory |
+The UI proxies `/api/*` requests to the API server at `localhost:3001`. Both processes terminate on Ctrl+C.
 
-## Web UI (Optional)
+### What the UI provides
 
-Dockit includes a web interface for managing entries, configuring sources, and browsing documentation.
+| Feature | Description |
+|---------|-------------|
+| **Entry management** | Create, edit, and delete documentation entries via a form |
+| **Source configuration** | Add/remove/reorder sources per entry — supports all 6 source types (ZIP, Maven, Antora, AsciiDoc, GitHub Markdown, Source Code) |
+| **Source form** | Mode selector (Git Repo / Local Dir / ZIP File), Graphify toggle with source path field |
+| **Build triggering** | One-click build with live streaming logs |
+| **Download script** | Export build as a self-contained `.sh` script (for CI/reproducible builds) |
+| **Document viewer** | Browse built HTML docs in the browser |
+| **Entry detail** | Shows all sources, graph status badge (Network icon when graphify is enabled), build history |
+| **Status badges** | Quick visual indicators for entry status (pending/building/ready/error) per source |
 
-```bash
-# Start dev servers
-dockit dev
-# Or: npm run dev
+### What it shows
 
-# Frontend → http://localhost:5173
-# Backend  → http://localhost:3001
-```
+The UI surfaces the same data as the CLI, but visually:
 
-1. Open http://localhost:5173 in your browser
-2. Click **New Entry** in the sidebar
-3. Add sources (including **Source Code** type) and click **Build Now**
-4. For doc sources with repos, toggle **Generate source code knowledge graph** and set the **Source Code Path**
-5. Use the embedded viewer to browse, or search across indexed content
+1. **Sidebar** — list of all entries with status badges
+2. **Entry page** — entry metadata (name, version, description) + sources list + build controls
+3. **Source editor** — configure type, URL/path, source path, graphify toggle
+4. **Build log** — real-time output stream during builds
+5. **Graph status** — which entries have knowledge graphs built
 
-### Build Modes
+### Architecture
 
-- **Build Now** — server-side processing with live log output
-- **Download Script** — exports a self-contained `.sh` script with all curl commands
+```
+Browser (port 5173) ←→ API Server (port 3001)
+                          ↓
+                     SQLite DB  +  LanceDB  +  ~/.dockit/
+```
 
-## Data Storage
+The UI communicates with the Express API via REST endpoints (`/api/entries`, `/api/sources`, `/api/build`, etc.). All data CRUD, search, and build operations are done through the same API that the CLI and MCP server use.
 
-All runtime data is stored in `~/.dockit/` by default:
+---
 
-| Path | Description |
-|------|-------------|
-| `~/.dockit/dockit.db` | SQLite database (entries, sources, builds) |
-| `~/.dockit/dockit.yaml` | User configuration (auto-created by `dockit init`) |
-| `~/.dockit/.lancedb/` | Vector search index (LanceDB) |
-| `~/.dockit/models/` | HuggingFace ONNX embedding model cache |
-| `~/.dockit/{entryId}/bundle/` | Built HTML documentation per entry |
-| `~/.dockit/{entryId}/sources/` | Raw source processing artifacts |
-| `~/.dockit/{entryId}/graph.json` | Knowledge graph (source-code entries) |
+## Offline / Air-Gapped Mode
 
-Override with the environment variable:
+Dockit is designed for full offline operation:
 
-```bash
-export DOCKIT_DATA_DIR=/custom/path   # all data goes here instead of ~/.dockit/
-```
+| Concern | Solution |
+|---------|----------|
+| **No internet** | All models bundled in npm package, LanceDB is embedded (Rust native) |
+| **Corporate proxy** | Set `HTTP_PROXY`/`HTTPS_PROXY` env vars |
+| **Pre-built indexes** | Build on connected machine, copy `~/.dockit/` to target |
+| **Embedding model** | Ships as ONNX (~88 MB). Caches to `~/.dockit/models/` |
+| **Source repos** | Clone once locally, reference via `localPath` in config |
+| **Maven Javadoc** | Download JAR once, reference via `localJar` or use local Maven settings |
 
-Configuration (`dockit.yaml`) is resolved in order:
-1. `~/.dockit/dockit.yaml` (user home, persisted by `dockit init`)
-2. Project root `dockit.yaml` (backward compatibility for development)
+---
 
 ## Architecture
 
 ```
-dockit/
+dockit/                          # npm package @lon-ask/dockit
+├── bin/
+│   ├── dockit.js                # CLI entry point (shebang node)
+│   ├── dockit-cli.ts            # Command router
+│   ├── commands/                # search, build, graph, init, get, list, dev, mcp
+│   └── utils.ts                 # Shared CLI helpers
 ├── apps/
-│   ├── server/          Express + TypeScript backend (port 3001)
+│   ├── server/                  # Express backend (port 3001)
 │   │   └── src/
-│   │       ├── core/domain/           Domain types & knowledge-graph types
-│   │       ├── core/ports/            IKnowledgeGraph, ISourceProcessor + ports
-│   │       ├── core/usecases/         BuildUseCase, ConfigUseCase, SearchUseCase
-│   │       ├── infrastructure/graph/  GraphifyKnowledgeGraph, GraphSearchDecorator
-│   │       ├── infrastructure/source-processors/  SourceCodeSourceProcessor + others
-│   │       └── routes/graph.ts        Graph REST endpoints
-│   └── client/          React + Vite + Tailwind CSS frontend (port 5173)
-├── bin/                 CLI entry point, graph commands, init command
+│   │       ├── core/            # Domain types, ports, use cases
+│   │       ├── infrastructure/  # SQLite, LanceDB, Graphify, processors
+│   │       ├── routes/          # REST API, graph endpoints, viewer
+│   │       └── services/        # Config loader, text extractor, normalizer
+│   └── client/                  # React + Vite web UI (port 5173)
 ├── packages/
-│   └── embeddings/      @dockit/embeddings — ONNX model wrapper (@huggingface/transformers)
-├── ~/.dockit/            Runtime data (created automatically on first run)
-│   ├── dockit.db              SQLite database
-│   ├── dockit.yaml            Entries/sources config (auto-created by `dockit init`)
-│   ├── .lancedb/              Vector search index
-│   ├── models/                HuggingFace ONNX embedding model cache
-│   ├── {entryId}/bundle/      Build outputs per entry
-│   ├── {entryId}/sources/     Raw source processing artifacts
-│   └── {entryId}/graph.json   Knowledge graph (source-code entries)
-├── dockit.yaml          Entries/sources config
-├── SKILL.md             LLM skill instructions
-├── GRAPHIFY_SOURCE_PLAN.md  Graphify feature plan
-└── package.json         npm workspace root
-```
-
-## API Overview
+│   └── embeddings/              # @lon-ask/dockit-embeddings
+│       └── model/               # all-MiniLM-L6-v2 ONNX (88 MB)
+├── scripts/
+│   └── mcp-wrapper.sh           # MCP server launcher
+├── dockit.yaml                  # Example config
+└── SKILL.md                     # LLM agent instructions
+```
+
+Runtime data (auto-created):
+```
+~/.dockit/
+├── dockit.db                    # SQLite (entries, sources, builds)
+├── dockit.yaml                  # Your config
+├── .lancedb/                    # Vector search index
+├── models/                      # Embedding model cache
+└── {entryId}/
+    ├── bundle/                  # Normalized HTML docs
+    ├── sources/                 # Raw processing artifacts
+    └── graph.json              # Knowledge graph
+```
+
+---
+
+## API Reference
 
 | Method | Path | Purpose |
 |--------|------|---------|
-| `GET`    | `/api/entries`                    | List entries |
-| `POST`   | `/api/entries`                    | Create entry |
-| `GET`    | `/api/entries/:id`                | Get entry detail + sources |
-| `PUT`    | `/api/entries/:id`                | Update entry |
-| `DELETE` | `/api/entries/:id`                | Delete entry + all data |
-| `POST`   | `/api/entries/:id/sources`        | Add source to entry |
-| `PUT`    | `/api/sources/:id`                | Update source |
-| `DELETE` | `/api/sources/:id`                | Remove source |
-| `POST`   | `/api/entries/:id/build`          | Trigger build |
-| `GET`    | `/api/entries/:id/build-status`   | Poll build progress |
-| `GET`    | `/api/entries/:id/cli-script`     | Download CLI script |
-| `GET`    | `/api/graph/:entry/query?q=...`   | Search knowledge graph nodes |
-| `GET`    | `/api/graph/:entry/path?from=...&to=...` | Find path between nodes |
-| `GET`    | `/api/graph/:entry/gods`          | List most connected nodes |
-| `GET`    | `/api/entries/:id/search?q=term`  | Search built docs |
-| `GET`    | `/api/bundle/:entryId/*`          | Serve bundled HTML |
+| `GET` | `/api/entries` | List entries |
+| `POST` | `/api/entries` | Create entry |
+| `GET` | `/api/entries/:id` | Get entry detail |
+| `PUT` | `/api/entries/:id` | Update entry |
+| `DELETE` | `/api/entries/:id` | Delete entry |
+| `POST` | `/api/entries/:id/sources` | Add source |
+| `PUT` | `/api/sources/:id` | Update source |
+| `DELETE` | `/api/sources/:id` | Remove source |
+| `POST` | `/api/entries/:id/build` | Trigger build |
+| `GET` | `/api/entries/:id/build-status` | Poll build |
+| `GET` | `/api/entries/:id/cli-script` | Download CLI script |
+| `GET` | `/api/graph/:entry/query?q=...` | Graph node search |
+| `GET` | `/api/graph/:entry/path?from=...&to=...` | Graph path find |
+| `GET` | `/api/graph/:entry/gods` | Graph god nodes |
+| `GET` | `/api/entries/:id/search?q=term` | Search docs |
+| `GET` | `/api/bundle/:entryId/*` | Serve HTML |
+
+---
 
 ## Tech Stack
 
 | Layer | Technology |
 |-------|-----------|
-| Frontend | React 19, TypeScript, Vite 6, Tailwind CSS 4, React Router 7 |
-| Backend | Express 4, TypeScript, tsx |
+| CLI | Node.js, tsx (TypeScript runtime) |
+| Backend | Express 4, TypeScript |
 | Database | SQLite via better-sqlite3 |
-| MCP | @modelcontextprotocol/server 2.0.0-alpha.2 |
-| HTML Parsing | node-html-parser |
+| Vector Search | LanceDB (embedded Rust) |
+| Embeddings | all-MiniLM-L6-v2 ONNX via @huggingface/transformers |
+| Frontend | React 19, Vite 6, Tailwind CSS 4 |
+| MCP | @modelcontextprotocol/server v2 |
+| HTML/MD Parse | node-html-parser, marked |
 | AsciiDoc | @asciidoctor/core |
+| Antora | @antora/cli + @antora/site-generator |
 | Archives | unzipper |
-| Build Pipeline | Antora CLI, Git, Maven dependency plugin |
-| Markdown | marked |
-| Vector Search | LanceDB embedded (Rust native), all-MiniLM-L6-v2 via @huggingface/transformers |
 | Knowledge Graph | Graphify (Tree-sitter AST, 15+ languages) |
+
+---
+
+## Credits
+
+Dockit was built with the assistance of the following LLMs and tools:
+
+| Contributor | Role |
+|------------|------|
+| **[OpenCode](https://opencode.ai)** | Primary development agent — architecture, code generation, code review, CLI tooling, MCP server, graph features, npm publishing pipeline |
+| **[DeepSeek](https://deepseek.com)** | Strategic architecture planning, feature design, documentation writing, test planning |
+
+Special thanks to:
+
+| Tool | Used for |
+|------|---------|
+| **[Graphify](https://github.com/safishamsi/graphify)** | Tree-sitter AST source code knowledge graphs |
+| **[LanceDB](https://lancedb.com)** | Embedded vector search |
+| **[OpenCode](https://opencode.ai)** | Interactive CLI agent framework that orchestrated the entire build pipeline |