v0.2.0 — Write tools (notes, tags, annotations)

What's new

DeepRead's MCP server now supports bidirectional Zotero: AI agents can not only read your library, they can save their insights back as notes, tags, annotations, and collection assignments.

5 write tools

• add_note — markdown child notes with optional title and user tags
• add_tag / remove_tag — manage tags on an item
• add_to_collection — move existing items into collections
• add_annotation — sticky-note comments on the first PDF of an item (with optional page label and color)

Safety

• Write tools are off by default. Tick Settings → DeepRead → "Allow write operations" to enable them. Read tools work as before.
• Every write is auto-tagged deepread:mcp. Use Zotero's tag selector to find/undo all model-made changes.
• The audit tag cannot be removed via MCP.

Workflow this enables

In Claude Code: "Read the Vaswani 2017 paper, write a 1-paragraph summary as a child note tagged 'attention-mechanism', and add the paper to my 'core-readings' collection." — one prompt, three tools, three writes, one new tag chain you can audit.

Compatibility

• Plugin id and pref namespace unchanged. v0.1.x users upgrade in place.
• New pref extensions.zotero-copilot.mcpAllowWrite defaults off — existing setups remain read-only until explicitly enabled.

See docs/MCP.md for the full tool reference and install snippets.

Full Changelog: v0.1.0...v0.2.0

v0.1.0 — MCP server for Claude Code / Cursor / Codex CLI

What's new

DeepRead now ships an MCP (Model Context Protocol) server. Use your existing Claude Code / Cursor / Codex CLI / Copilot subscription to chat with your Zotero library — no separate API key needed.

Install

Zotero plugin — download zotero-copilot-0.1.0.xpi and install via Tools → Plugins → ⚙ → Install Plugin From File.

MCP server (after the plugin) — turn on Settings → DeepRead → Enable MCP server, then in your IDE:

• Claude Code: claude mcp add --scope user deepread -- npx -y deepread-mcp
• Cursor: click "Add to Cursor" in plugin settings (one-click deeplink)
• Codex CLI: paste the snippet shown in plugin settings into ~/.codex/config.toml
• Other MCP clients: copy the generic JSON config from plugin settings

See docs/MCP.md for full details.

7 tools exposed

search_library, get_item, get_item_fulltext, list_collections, search_collection, rag_query, get_annotations

rag_query reuses the same embedding index the in-Zotero sidebar builds — no double indexing.

Other changes

• Restructured to npm-workspaces monorepo (packages/{shared, zotero-plugin, mcp-server})
• All previous features unchanged: sidebar chat, collection RAG overlay, prefs pane, copy controls, collapsible sidebar
• Same plugin id zotero-copilot@xiangweiw.dev and same pref namespace, so 0.0.x users upgrade in place without losing API keys / collection indexes

Known caveats

• MCP server is off by default — toggle it in Settings → DeepRead before connecting any client
• Tools are read-only — annotation write-back lands in the next release
• Long RAG queries: stdio bridge has a soft ~60s timeout in some clients; rag_query returns top-K excerpts so the model synthesizes the answer (rather than the server doing slow synthesis)

Full Changelog: v0.0.2...v0.1.0

v0.0.2 — Initial public release

First public release of DeepRead.

Install

1. Download zotero-copilot-0.0.2.xpi below.
2. In Zotero: Tools → Plugins → ⚙ (gear) → Install Plugin From File...
3. Pick the downloaded file. Restart Zotero if prompted.
4. Open Settings → DeepRead and set your Anthropic or Gemini API key.

What's included

• Single-paper chat sidebar in the PDF reader (Anthropic Claude / Google Gemini, streaming)
• Right-click "Ask DeepRead" on PDF text selections
• Collection-level RAG: right-click any collection → "Analyze with DeepRead" → draggable / resizable floating chat with retrieval over all papers in the collection
• Native Zotero preferences pane
• Save chat transcripts as Zotero child notes
• Collapsible sidebar, copy / select-all / raw-text toolbar on every assistant message

Compatibility

• Tested on Zotero 9.0.1 / macOS 14
• Plugin id: zotero-copilot@xiangweiw.dev (kept for backward compat with internal pref keys)
• Manifest accepts Zotero 6.999 → *; should work on Zotero 7.x and later

Known limitations

• Drag-to-select inside chat bubbles is unreliable in Zotero's chrome iframe — use the toolbar buttons (✎ / ⊟ / ⧉)
• Gemini free tier has rate limits on some models; gemini-2.5-flash works
• Collection RAG requires Zotero full-text indexing of PDFs (auto-triggered)

Full Changelog: https://github.com/XiangweiW/deepread/commits/v0.0.2