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It gives AI assistants (and you) a persistent, queryable memory — both for **written knowledge** (wiki pages, articles, PDFs) and **code structure** (functions, classes, call graphs, imports across 15+ languages).\n\n---\n\n## Requirements\n\n- [OpenCode](https://opencode.ai) installed and on PATH\n- [Obsidian](https://obsidian.md) desktop app installed and running\n- [Obsidian CLI](https://obsidian.md/cli) installed and on PATH (`obsidian --version` should work)\n- [Bun](https://bun.sh) (for the CLI and MCP server)\n\n---\n\n## Quick Start\n\n```bash\nnpx @cubocompany/opengem init\n```\n\nThe setup wizard checks prerequisites, lets you pick your vault, writes config to `opencode.json`, and initializes the wiki folder structure — no JSON editing required.\n\nThen, inside any project:\n\n```bash\nopengem graph          # index the current directory\nopengem watch          # keep the graph live as you code\n```\n\n---\n\n## Code Knowledge Graph\n\nOpenGem parses your source code into a **navigable knowledge graph** — functions, classes, modules, and their relationships (calls, imports, contains). The graph is stored locally at `.opengem/graph-state.json` and updated incrementally.\n\n### Why a knowledge graph?\n\nYour raw source files are the full, uncompressed representation of your codebase. The knowledge graph is the **distilled, queryable memory** — symbols, relationships, and communities extracted once, reused across every AI session.\n\nInstead of reading entire files, your AI assistant can ask:\n- \"What calls `buildGraph`?\" → one graph lookup, no file reads\n- \"What does `runGraphIndexTool` depend on?\" → instant call chain, no grepping\n\nThe graph is your token-efficient entry point to the codebase.\n\n### Supported languages\n\n| Category | Languages |\n|---|---|\n| Dedicated extractors | TypeScript, JavaScript, Python |\n| Generic extractors | Go, Rust, Java, C, C++, Ruby, Kotlin, Swift, Lua, Scala, PHP, C# |\n| Documents | Markdown (`.md`/`.mdx`), PDF |\n\nMarkdown headings become `section` nodes; wikilinks and relative links become `imports` edges. PDFs are parsed page-by-page with heading detection.\n\n### CLI commands\n\n```bash\nopengem graph [dir]          # index a directory (default: current dir)\nopengem watch [dir]          # watch for changes and re-index incrementally\nopengem query <search>       # search nodes by name or file\nopengem explain <symbol>     # show all connections for a symbol\nopengem path <from> <to>     # find the shortest path between two symbols\n```\n\n**Examples:**\n\n```bash\n# Index just the src/ folder\nopengem graph ./src\n\n# Find everything related to \"buildGraph\"\nopengem query buildGraph\n\n# Who calls parseFile, and what does it call?\nopengem explain parseFile\n\n# How does the CLI reach the community detection algorithm?\nopengem path main detectCommunities\n```\n\n**Sample output — `opengem explain buildGraph`:**\n\n```\n  buildGraph  (function)  lib/graph/graph-builder.ts:41\n\n  Incoming (3):\n    ← calls      cmdGraph       (cli.ts)\n    ← calls      runGraphIndexTool  (tools/graph-index.ts)\n    ← contains   lib/graph/graph-builder.ts\n\n  Outgoing (8):\n    → calls      collectFiles   (lib/graph/graph-builder.ts)\n    → calls      getParser      (lib/graph/ast-parser.ts)\n    → calls      extractGeneric (lib/graph/ast-generic.ts)\n    → calls      detectCommunities  (lib/graph/graph-community.ts)\n    ...\n```\n\n### Watch mode\n\n```bash\nopengem watch ./src\n```\n\nRe-indexes only the files that changed (400 ms debounce). On deletion, forces a full re-index to remove stale nodes. Press `Ctrl+C` to stop.\n\n### Git hook\n\nKeep the graph in sync automatically after every commit:\n\n```bash\nopengem hooks install     # adds post-commit hook\nopengem hooks uninstall   # removes it\n```\n\n---\n\n## opengem-out/ — Visual Output\n\nEvery `opengem graph` run generates a human-readable output folder alongside the machine-readable state:\n\n```\nopengem-out/\n  graph.html        ← interactive vis.js visualization (open in browser)\n  GRAPH_REPORT.md   ← god nodes, communities, language stats, suggested questions\n  graph.json        ← clean node/edge/community export for external tools\n```\n\nOpen `opengem-out/graph.html` in any browser — no server required. Nodes are sized by connectivity, colored by community, and searchable. The report helps you understand the architecture at a glance and surfaces the most-connected symbols before you start exploring.\n\n---\n\n## .opengemignore\n\nAdd a `.opengemignore` file to your project root to exclude paths from indexing. Uses the same gitignore syntax:\n\n```gitignore\n# Exclude generated files\ngenerated/\n*.pb.go\n\n# Exclude test fixtures\n**/__fixtures__/\ntests/snapshots/\n\n# Exclude vendored code\nvendor/\nthird_party/\n```\n\nNode modules, `.git`, `dist`, `build`, and other common non-source directories are always excluded regardless of `.opengemignore`.\n\n---\n\n## MCP Server\n\nOpenGem ships a standalone **MCP server** (`opengem-mcp`) that exposes the knowledge graph to any MCP-compatible AI client — Claude Desktop, Cursor, or any other tool that supports the Model Context Protocol.\n\n```bash\nnpx opengem-mcp\n```\n\n### Tools\n\n| Tool | Description |\n|---|---|\n| `graph_index` | Index a directory into `.opengem/graph-state.json` |\n| `graph_query` | Search nodes by name or file path |\n| `graph_explain` | Show all connections for a symbol |\n| `graph_path` | Find the shortest path between two symbols |\n\n### Setup\n\n**Claude Desktop** (`~/Library/Application Support/Claude/claude_desktop_config.json`):\n\n```json\n{\n  \"mcpServers\": {\n    \"opengem\": {\n      \"command\": \"npx\",\n      \"args\": [\"opengem-mcp\"]\n    }\n  }\n}\n```\n\n**OpenCode** (`opencode.json` or `~/.config/opencode/opencode.json`):\n\n```json\n{\n  \"mcp\": {\n    \"opengem\": {\n      \"type\": \"stdio\",\n      \"command\": \"npx\",\n      \"args\": [\"opengem-mcp\"]\n    }\n  }\n}\n```\n\nRun `opengem mcp` to see the full setup instructions.\n\n---\n\n## AI Tool Integration\n\nConfigure OpenGem in all your AI tools at once:\n\n```bash\nopengem install            # configure everything (claude + cursor + opencode)\nopengem install claude     # add graph instructions to CLAUDE.md\nopengem install cursor     # write .cursor/rules\nopengem install opencode   # register plugin in opencode.json\n```\n\n`install claude` appends a section to your project's `CLAUDE.md` that tells Claude Code how to use the graph CLI for precise codebase lookups — reducing hallucination and broad file searches.\n\n---\n\n## OpenCode Slash Commands\n\nWhen loaded as an OpenCode plugin, OpenGem registers slash commands directly in the chat UI:\n\n| Command | Action |\n|---|---|\n| `/opengem-graph-index` | Index this project's code into your Obsidian graph |\n| `/opengem-find <name>` | Search the code graph for a symbol or file |\n| `/opengem-explain <symbol>` | Explain the connections of a symbol |\n| `/opengem-path <from> <to>` | Find the path between two symbols |\n| `/opengem-wiki-add <url>` | Add an article to your wiki |\n| `/opengem-wiki-search <query>` | Search your wiki |\n| `/opengem-wiki-save` | Save the last answer to your wiki |\n| `/opengem-wiki-lint` | Check your wiki for broken links |\n| `/opengem-help` | List all available OpenGem tools |\n| `/opengem-doctor` | Verify Obsidian CLI and app status |\n\nArgs are passed directly: `/opengem-find buildGraph` → searches for `buildGraph` without a follow-up prompt.\n\n---\n\n## Wiki\n\nOpenGem builds a structured wiki inside your Obsidian vault where AI can store and retrieve knowledge across sessions.\n\n### Structure\n\n`opengem init` creates:\n\n```\nwiki/\n  INDEX.md       ← auto-generated index of all wiki pages\n  LOG.md         ← append-only log of every ingest and query\nschema/\n  SCHEMA.md      ← conventions for wiki pages (edit to customize)\nraw/\n  .keep          ← original sources go here, untouched\n```\n\n### Natural language usage\n\n| What you say | What happens |\n|---|---|\n| \"Add this article to my wiki: https://...\" | Fetches, ingests to `raw/` and `wiki/` |\n| \"What do I know about X?\" | Searches wiki, answers with citations |\n| \"Update my wiki page on Y\" | Rewrites the page with new information |\n| \"Check my wiki for issues\" | Runs lint — broken links, missing metadata |\n| \"Refresh my wiki index\" | Rebuilds `wiki/INDEX.md` |\n\n---\n\n## OpenCode Tools Reference\n\n### Code graph\n\n| Tool | Description |\n|---|---|\n| `obsidian_graph_index` | Index a codebase into the Obsidian graph (creates notes per node) |\n| `obsidian_graph_query` | Search graph nodes by name, kind, or community |\n| `obsidian_graph_neighbors` | List incoming/outgoing edges for a node |\n| `obsidian_graph_path` | Find the shortest path between two nodes |\n\n### Wiki\n\n| Tool | Description |\n|---|---|\n| `obsidian_wiki_init` | Set up wiki folder structure |\n| `obsidian_wiki_ingest` | Save a source to `raw/` and create a `wiki/` page |\n| `obsidian_wiki_update` | Rewrite a wiki page |\n| `obsidian_wiki_search_cited` | Search wiki with citations |\n| `obsidian_wiki_save_answer` | Save an answer to `wiki/answers/` |\n| `obsidian_wiki_refresh_index` | Regenerate `wiki/INDEX.md` |\n| `obsidian_wiki_lint` | Check for broken links and missing metadata |\n\n### Vault\n\n| Tool | Description |\n|---|---|\n| `obsidian_read` | Read a note |\n| `obsidian_search` | Search vault content |\n| `obsidian_create_note` | Create a new note |\n| `obsidian_append_note` | Append text to a note |\n| `obsidian_set_property` | Set a frontmatter property |\n| `obsidian_backlinks` | List backlinks to a note |\n| `obsidian_tags` | List all tags |\n| `obsidian_tag_notes` | List notes with a specific tag |\n\n### Developer & diagnostics\n\n| Tool | Description |\n|---|---|\n| `obsidian_env_doctor` | Check CLI, app, vault, and skills status |\n| `obsidian_eval` | Execute JavaScript in Obsidian |\n| `obsidian_dev_errors` | Show captured errors |\n| `obsidian_dev_console` | Show captured console messages |\n| `obsidian_dev_screenshot` | Take a screenshot |\n| `obsidian_dev_dom` | Query DOM elements |\n| `obsidian_dev_css` | Inspect CSS |\n| `obsidian_plugins` | List installed plugins |\n| `obsidian_plugin_reload` | Reload a plugin |\n\n---\n\n## Configuration\n\nAdd to `opencode.json` (project) or `~/.config/opencode/opencode.json` (global):\n\n```json\n{\n  \"plugin\": [\n    [\"@cubocompany/opengem\", {\n      \"defaultVault\": \"My Vault\"\n    }]\n  ]\n}\n```\n\nOr run `opengem install opencode` to have it written for you.\n\n### Options\n\n| Option | Type | Default | Description |\n|---|---|---|---|\n| `defaultVault` | `string` | auto-detected | Target vault for all operations |\n\nVault resolution order: explicit `vault` arg → `defaultVault` in config → active vault from `obsidian vault` → single vault auto-select.\n\n---\n\n## Development\n\n```bash\ngit clone https://github.com/cubocompany/opengem\ncd opengem\nbun install\nbun run check     # TypeScript type-check\nbun run build     # builds dist/index.js (plugin), dist/cli.js, dist/mcp.js\nbun test\n```\n\n### Project structure\n\n```\nsrc/\n  index.ts              ← OpenCode server plugin (tools + slash commands + context injection)\n  cli.ts                ← opengem CLI (graph, watch, query, explain, path, hooks, install, mcp)\n  mcp.ts                ← opengem-mcp MCP server\n  tui.ts                ← OpenCode TUI plugin\n  lib/\n    graph/\n      ast-parser.ts         ← language detection + tree-sitter parser cache\n      ast-js.ts             ← JS/TS dedicated extractor\n      ast-py.ts             ← Python dedicated extractor\n      ast-generic.ts        ← config-driven extractor for 12 languages\n      ast-md.ts             ← Markdown extractor (headings, wikilinks)\n      ast-pdf.ts            ← PDF extractor (unpdf/pdfjs)\n      language-configs.ts   ← per-language node type and name strategy configs\n      graph-builder.ts      ← incremental build pipeline (all languages)\n      graph-store.ts        ← state persistence + graphology construction\n      graph-community.ts    ← Louvain community detection\n      graph-paths.ts        ← node ID ↔ Obsidian note name conversion\n      graph-community.ts    ← Louvain community detection\n      ignore-parser.ts      ← .opengemignore gitignore-style rule loader\n      output-renderer.ts    ← opengem-out/ generator (graph.html, GRAPH_REPORT.md, graph.json)\n      note-renderer.ts      ← renders graph nodes as Obsidian markdown notes\n    wiki.ts / config.ts / cli.ts / types.ts\n  tools/                ← individual tool implementations\n```\n\n---\n\n## License\n\nMIT\n","readmeFilename":"README.md"}