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MCP server for your knowledge base — Zotero, Obsidian, and Apple Notes (macOS) over a resident native C++ search core (BM25 + passage retrieval, mixed search; stdio + Streamable HTTP)","maintainers":[{"name":"docsagent","email":"awadb.vincent@gmail.com"}],"readme":"# DocsAgent MCP — Zotero, Obsidian & Apple Notes for AI agents 📚⚡\n\n**DocsAgent gives AI agents instant, private access to your personal knowledge base.**\n**`@docsagent/docsagent`** is the spec-driven **MCP (Model Context Protocol) server** that lets\nany AI agent — Claude Desktop, Cursor, Cline, Qwen Code, or any MCP client — search, read, and\nwrite your **Zotero** library, **Obsidian** vault, and **Apple Notes** (macOS) through a resident\n**C++ search engine**. BM25 full-text search + query-ranked passage retrieval over **1,000+ PDFs**\nat **~15 ms**, fully local (RAG-ready knowledge base).\n\n- 🔒 **Local-first & private** — the engine reads your Zotero library, Obsidian vault, and\n  Apple Notes store directly on your machine. Your notes and PDFs never leave it.\n- 🗂 **Three sources, one query** — Zotero items/annotations/notes, Obsidian vaults, and\n  Apple Notes (macOS only); mixed search fuses all three by reciprocal rank.\n- ⚡ **Native C++ search core** — inverted-index BM25 + passage ranking, millisecond lookup,\n  low memory footprint (160–227 MB for a 1,500-paper library).\n- 🧩 **8 MCP tools** — 5 read + 3 write, with JSON-schema validated arguments, token budgets,\n  result dedup, and a three-layer write safety gate.\n- 🌐 **Two transports** — stdio for local MCP clients, Streamable HTTP for remote deployment\n  (origin checks, API-key / OAuth 2.0 token introspection, per-request RBAC, `/health` probe).\n- 🐍 **Two shells, one core** — this TypeScript package and a feature-equal\n  [Python wrapper](python/) ship the same tools over the same JSON-RPC contract.\n\n---\n\n## Architecture\n\n```\nMCP Client (Claude Desktop / Cursor / Cline / Qwen Code / any MCP host)\n        │  stdio (local)   or   Streamable HTTP  /mcp  (remote)\n        ▼\nMCP shell  ← this package (@docsagent/docsagent / docsagent)\n   · tool schemas (spec-driven), argument validation, token budget, dedup\n   · write orchestration via the Zotero local API, write safety gate, RBAC\n   · group-library sync via the Zotero Web API\n        │  JSON-RPC 2.0 over HTTP ({coreHost}:{httpPort}/rpc, cpp-httplib)\n        ▼\nDocsAgent Core (resident C++ engine)\n   · reads ~/Zotero/zotero.sqlite + storage/, an Obsidian vault, and (macOS) the\n     Apple Notes store — directly on your machine\n   · builds & serves one index per source (BM25 + passage ranking); mixed search\n     (source \"all\") fuses them by reciprocal rank (RRF, k=60)\n```\n\nThe shell **never spawns the core** during tool calls and never touches your source files.\nThe core runs as a background service and stays available across MCP client restarts.\nTool schemas and error codes: [spec/](spec/).\n\n---\n\n## Quick Start\n\n### 1. Start the core\n\n```bash\nnpx @docsagent/docsagent start            # spawn the bundled core for your platform\nnpx @docsagent/docsagent status           # pid / endpoint / version\n```\n\nPython shell (same verbs, under the `core` subcommand):\n\n```bash\npip install ./python                      # build the wheel locally (PyPI upload pending)\ndocsagent core start\n```\n\n(`core stop` / `core restart` also available. The core indexes every configured source — your\nZotero data directory, your Obsidian vault, and (macOS) Apple Notes — and serves JSON-RPC on\n`http://0.0.0.0:23120/rpc`.)\n\n### 2. Configure your MCP client\n\nClaude Desktop / Cursor / Cline / Qwen Code (`mcpServers`):\n\n```json\n{\n  \"mcpServers\": {\n    \"docsagent\": {\n      \"command\": \"npx\",\n      \"args\": [\"-y\", \"@docsagent/docsagent\"]\n    }\n  }\n}\n```\n\nPython shell (same tools, same contract, installed from this repo) — `mcpServers`:\n\n```json\n{\n  \"mcpServers\": {\n    \"docsagent-py\": {\n      \"command\": \"docsagent\"\n    }\n  }\n}\n```\n\nInstall the Python package first (step 1) so `docsagent` is on your PATH.\n\nOn startup the shell connects to the core, loads sources, and checks index status. If the\ncore is not running it fails fast with startup instructions — it never spawns anything.\n\n---\n\n## MCP Tools (external API)\n\n8 tools, 5 read + 3 write. Schemas are the single-sourced contract in\n[`spec/tools/*.json`](spec/tools) (mirrored into both packages); arguments are validated\nbefore handlers run and failures map to typed docsagent error codes.\n\n### `list_sources`\nEvery searchable source with capabilities, supported targets/includes/browse modes,\nfilters, and document counts. **Call this first.**\n\nSources today: `zotero` (targets `items`, `annotations`, `notes`; collections/tags browse),\n`obsidian` (a vault — notes as items, folders/tags browse), and `apple-notes` (**macOS only** —\nthe engine omits the source on other platforms). The vault is found at\n`~/Documents/Obsidian Vault` (override with `DOCSAGENT_OBSIDIAN_VAULT`); Apple Notes is read\nfrom the system Notes store (override with `DOCSAGENT_APPLE_NOTES_DB`).\n\n### `search`\nCross-entry search over one source (items, annotations, and notes).\n\n| Parameter | Type | Notes |\n|---|---|---|\n| `query` | string | plain keywords or phrases; required unless `mode=grep` |\n| `mode` | `relevance` \\| `grep` | BM25 relevance by default; `grep` scans for a **literal** pattern without tokenization or ranking |\n| `pattern` | string, required when `mode=grep` | literal string to scan for |\n| `caseSensitive`, `wholeWord`, `maxMatches` | | `mode=grep` only: ASCII case folding, `[A-Za-z0-9_]` word boundaries, hit cap total |\n| `target` | `\"items\" \\| \"annotations\" \\| \"notes\"` or array | default `items` |\n| `depth` | `ids` \\| `snippets` \\| `full` | snippets by default (BM25-ranked passages) |\n| `filters` | object | `tags`, `yearFrom`/`yearTo`, `itemType`, `authors`, `colors`, `containerId`, `titleContains` |\n| `k`, `snippetsPerResult`, `max_tokens` | numbers | ranking depth and token budget (`mode=grep`: max documents, max hit windows per document) |\n\nReturns `results[]` with global ids (`zotero:KEY`, `obsidian:<path>`, `apple-notes:<uuid>`),\ntitles, relevance, snippets; multi-target\nsearches group by target. In `mode=grep` each result carries `matchCount` and `snippets[]`\nhit windows (`hits[]` with `line`/`column`/`offset`, and meta hits tagged with `field`),\n`relevance` is `0`, and the response adds `totalMatches`. Results are deduped (id, then\nnormalized title + year) and packed under a token budget.\n\n`search` runs against `config.defaultSource` (default `zotero`). **Mixed search** is a core\ncapability: pass `source: \"all\"` to the core's `search` / `grep` methods and every source is\nranked independently, then fused with **reciprocal rank fusion** (k=60) — each hit is tagged\nwith its source. BM25 scores are not comparable across corpora, so fusion is rank-based.\n\n### `get_content`\nRead one entry. `mode=passages` (query-ranked passages, `k`) or `mode=fulltext`\n(offset pagination with `nextOffset`). Notes return their body with tags and metadata.\n\n### `get_metadata`\n`include`: `metadata`, `abstract`, `annotations`, `notes`, `citation` (bibtex / csljson /\nformatted via `citationFormat`/`citationStyle`). Notes are packed under the token budget.\n\n### `list_library`\nBrowse modes: `collections` (drill-down via `parentId`), `items` (by `containerId`),\n`tags`, `saved_searches`, `standalone_notes`. Browse modes are per source — Zotero exposes\nall of these, while Obsidian and Apple Notes expose `folders` (drill-down) / `tags` / `items`.\n\n### Write tools (three-layer safety gate)\n\n| Tool | What it does | Key arguments |\n|---|---|---|\n| `import_item` | Import local PDFs or resolve DOI / ISBN / arXiv IDs (via the Zotero translation server); optional `autoClassify` suggests collections | `paths` \\| `identifiers`, `containerId`, `autoClassify`, `confirmed` |\n| `add_note` | Add a Markdown child note to an item (converted to Zotero note HTML), with orphan verification and rollback | `id`, `content`, `tags`, `confirmed` |\n| `batch_modify` | Bulk `add_to_collection` / `remove_from_collection` / `add_tags` / `remove_tags` on up to 200 items in batches of 50 | `action`, `ids`, `containerId`, `tags`, `confirmed` |\n\nWrite tools target **Zotero sources only** — the Obsidian and Apple Notes sources are read-only.\n\nWrite safety gate (spec/algorithms/write-gate.md): **layer 1** write tools are not\nregistered unless `enableWrites=true`; **layer 2** `confirmed=false` returns a preview and\nconsumes no rate-limit quota; **layer 3** confirmed writes consume a per-hour rate limit\n(default 30/h). Anything above 20 items in `batch_modify` additionally reports\n`requiresConfirmation` in the preview.\n\n---\n\n## Engine performance\n\nThe C++ engine powers [PapersGPT](https://www.papersgpt.com/zh) — the same index and\nretrieval stack ships in this MCP server. Benchmark on a real Zotero installation\n([full write-up](https://www.papersgpt.com/zh/blogs/papersgpt-search-performance-benchmark)):\n\n| Metric | Mac (Intel i9) | Windows VM (4C8G) |\n|---|---|---|\n| Library size | 1,506 PDFs (4.5 GB on disk) | 500+ PDFs |\n| **Index build time** | **141 s** | a few seconds |\n| **Memory (agent process)** | **227 MB** | **160 MB** |\n| **Average retrieval latency** | **~15 ms** | **~15 ms** |\n\n- Indexing cost scales roughly **linearly** with library size; retrieval latency stays\n  **constant** — a 10,000-paper library (~30 GB) indexes in about 15–20 minutes, and\n  everyday search stays at **~15 ms**.\n- For comparison: a typical web page load takes 1,000–3,000 ms; a blink of an eye is\n  100–150 ms. PapersGPT answers in ~15 ms, fully offline.\n- Privacy: your library never leaves your machine.\n\n## Configuration\n\nConfig lives at `~/.docsagent/config.json` (or `$DOCSAGENT_CONFIG`) — one file shared by\nthe JS shell, the Python wrapper, and the C++ core. Validated against\n[`spec/config.json`](spec/config.json).\n\n| Key | Default | Description |\n|---|---|---|\n| `coreHost` | `0.0.0.0` | Address the core binds and the shell dials |\n| `httpPort` | `23120` | Core HTTP port (`POST /rpc`) |\n| `coreBinary` | `\"\"` | Optional explicit path to the core binary |\n| `zoteroDataDir` | `~/Zotero` | Zotero data directory |\n| `zoteroApiUrl` | `http://localhost:23119/api` | Zotero local API (write orchestration) |\n| `zoteroGroups` | `[]` | Group libraries to sync from zotero.org |\n| `enableWrites` | `false` | Register the three write tools |\n| `writeRateLimitPerHour` | `30` | Confirmed-write rate limit |\n| `maxTokensPerTool` | `4000` | Token budget per tool result |\n| `defaultSource` | `zotero` | Source the shell searches and resolves id prefixes in (`zotero`, `obsidian`, `apple-notes`) |\n| `transport` | `stdio` | `stdio` or `streamable-http` |\n| `httpListenAddr` | `0.0.0.0:8080` | Listen address for streamable-http (`/mcp`) |\n| `authMode` / `authConfig` | `none` | `api-key` or `oauth2` (RFC 7662) + `allowedOrigins` |\n| `rbacRoles` | `{}` | role → allowed tool names (per-request RBAC on HTTP) |\n| `logLevel` | `info` | `debug` / `info` / `warn` / `error` |\n\n---\n\n## Distribution\n\n| Channel | Package | Bundled core | Size |\n|---|---|---|---|\n| npm (JS/TS shell) | `@docsagent/docsagent` | all platforms in `bin/` | ~70 MB tarball |\n| PyPI (Python shell) | `docsagent` (`pip install ./python`) | same binaries in the wheel | ~65 MB wheel |\n\nBundled core platforms: **macOS** universal (Intel + Apple Silicon), **Windows** x64\n(x86_64), **Linux** x64 (x86_64) — Linux ARM is **not** supported. Source availability:\nZotero and Obsidian work on every platform; **Apple Notes is macOS-only** (`list_sources`\nomits it elsewhere).\n\nBoth shells read the same config and talk to the same core — pick either (or both) as\nyour MCP distribution channel. Core lifecycle (`start` / `stop` / `restart` / `status`)\nis available from both CLIs.\n\n## Links\n\n- [spec/](spec/) — the single-sourced contract: 8 tool schemas, 23 JSON-RPC methods,\n  error codes + suggested calls, config schema\n- [PapersGPT search performance benchmark](https://www.papersgpt.com/zh/blogs/papersgpt-search-performance-benchmark)\n- [Zotero](https://www.zotero.org/) · [Model Context Protocol](https://modelcontextprotocol.io)\n\n## License\n\nApache-2.0\n","readmeFilename":"README.md"}