Cline rules

1# PubMed Search MCP Project Rules
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3These rules are meant for Cline usage in the PubMed Search MCP repository.
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5## Goals
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7- Provide a robust MCP server for biomedical literature search, analysis, full-text access, and citation export.
8- Make MCP `unified_search` the default agent entrypoint while preserving specialized tools for PICO, MeSH, full text, citations, and pipelines.
9- Keep `pubmed_search.api` as the stable Python SDK facade for external package/notebook callers.
10- Keep outputs useful for downstream agents and for Zotero Keeper imports.
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12## Repo Layout
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14- `src/pubmed_search/domain/`: domain entities and value objects.
15- `src/pubmed_search/application/`: search, export, pipeline, and analysis use cases.
16- `src/pubmed_search/infrastructure/`: external clients and source integrations.
17- `src/pubmed_search/presentation/mcp_server/`: MCP server, tools, prompts, and resources.
18- `tests/`: pytest suite.
19- `.claude/skills/`: user-facing research skills.
20- `.cline/skills/` and `.clinerules/`: Cline harness assets.
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22## Canonical Commands
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24- `uv run ruff check .`
25- `uv run ruff format --check .`
26- `uv run mypy src/ tests/`
27- `uv run pytest`
28- `uv run python scripts/count_mcp_tools.py --update-docs`
29- `python3 scripts/check_cline_skills.py`
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31## Safety / Hygiene
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33- Avoid editing generated outputs unless the generator was run intentionally.
34- Never commit NCBI API keys, Semantic Scholar keys, CORE keys, OpenAlex keys, cookies, or institutional resolver secrets.
35- Avoid destructive git operations unless explicitly requested.
36- Keep network-dependent behavior mockable and rate-limit aware.
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38## Prefer Existing Patterns
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40- Reuse source adapters and registry abstractions instead of adding one-off HTTP calls.
41- Keep MCP tools small and delegate behavior to application services.
42- Keep backward-compatible aliases where agents already consume fields.
43- Update tool docs and user-facing skills when tool contracts change.
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