Cline rules

1---
2paths:
3  - "src/pubmed_search/presentation/mcp_server/**"
4  - "src/pubmed_search/application/**"
5  - "src/pubmed_search/infrastructure/sources/**"
6  - "scripts/count_mcp_tools.py"
7  - ".claude/skills/pubmed-mcp-tools-reference/SKILL.md"
8---
9 
10# PubMed MCP Tool Rules
11 
12## Tool Contract Rules
13 
14- Keep `unified_search` as the primary search facade.
15- Preserve session-aware flows: cached articles, last PMIDs, search history, and pipeline state.
16- Return source counts and warnings when a source fails or contributes zero results.
17- Keep output formats stable for markdown, JSON, RIS, BibTeX, CSV, and MEDLINE.
18- Do not remove old fields without tolerating them for at least one release cycle.
19 
20## Research Workflow Rules
21 
22- Use `generate_search_queries` and `analyze_search_query` before complex/systematic searches.
23- Use `parse_pico` for clinical comparison questions.
24- Use `get_fulltext`, `get_article_figures`, and institutional access tools only when full-text retrieval is requested.
25- Export to RIS for Zotero/EndNote and BibTeX for LaTeX workflows.
26 
27## Documentation Sync
28 
29When tools are added, removed, or renamed:
30 
31- Run `uv run python scripts/count_mcp_tools.py --update-docs`.
32- Update relevant `.claude/skills/pubmed-*` skills.
33- Update `.github/agents/research.agent.md` if the research flow changes.
34- Add or update MCP protocol tests.
35