Cline rules

1# Zotero Keeper Project Rules
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3These rules are meant for Cline usage in the Zotero Keeper repository.
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5## Goals
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7- Build a local MCP toolkit that combines Zotero reference management with PubMed literature search.
8- Keep the user path simple: VS Code extension setup should install Python, packages, MCP definitions, and assistant assets without manual glue.
9- Preserve research safety: ask before importing into Zotero collections, avoid duplicates, and keep source metadata traceable.
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11## Repo Layout
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13- `mcp-server/src/zotero_mcp/`: Zotero Keeper Python MCP server.
14- `mcp-server/tests/`: unit and integration tests for the Zotero server.
15- `external/pubmed-search-mcp/`: PubMed Search MCP submodule used by the extension.
16- `vscode-extension/`: VS Code extension that registers both MCP servers and installs assistant assets.
17- `.github/`: Copilot instructions, agents, bylaws, and CI/release workflows.
18- `.claude/skills/` and `.cline/skills/`: assistant-facing operational skills.
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20## Canonical Commands
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22- Zotero server checks: `cd mcp-server && uv run pytest`
23- Zotero lint/type checks: `cd mcp-server && uv run ruff check . && uv run mypy src --ignore-missing-imports`
24- Extension checks: `cd vscode-extension && npm run sync-assets && npm run compile && npm test`
25- VSIX package smoke: `cd vscode-extension && npm run package`
26- Diff hygiene: `git diff --check`
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28## Safety / Hygiene
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30- Avoid editing generated outputs: `vscode-extension/out/`, `dist/`, `.venv/`, `.pytest_cache/`, `__pycache__/`.
31- Never print or commit secrets from `.env`, NCBI API keys, Zotero credentials, or key files.
32- Do not use destructive git commands unless the user explicitly asks.
33- Submodule changes under `external/pubmed-search-mcp/` must be intentional and called out in status.
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35## Prefer Existing Patterns
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37- Keep MCP tool outputs backward-compatible when possible.
38- Use `import_articles` for PubMed-to-Zotero import flows unless a legacy path is explicitly requested.
39- Keep extension bundled asset sources and `vscode-extension/resources/repo-assets/` in sync via `npm run sync-assets`.
40- Start context reads with `memory-bank/activeContext.md`, `ARCHITECTURE.md`, and `docs/COLLABORATION_WORKFLOW.md` when the task is architectural.
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