| Dimension | Shared | Only in A | Only in B | Overlap |
|---|---|---|---|---|
| Sections | 0 | 6 | 7 | 0% |
| Commands | 0 | 6 | 1 | 0% |
| Section tags | 1 | 4 | 1 | 17% |
What each file covers
Sections
0 shared · 6 only in A · 7 only in B- − PubMed Search MCP Project Rules
- − Goals
- − Repo Layout
- − Canonical Commands
- − Safety / Hygiene
- − Prefer Existing Patterns
- + Zotero + PubMed MCP Codex Harness
- + Goal
- + Working Style
- + Core Workflow
- + Repository Work
- + Guardrails
- + Related Files
Commands
0 shared · 6 only in A · 1 only in B- − uv run ruff check .
- − uv run ruff format --check .
- − uv run mypy src/ tests/
- − uv run pytest
- − uv run python scripts/count_mcp_tools.py --update-docs
- − python3 scripts/check_cline_skills.py
- + npm run sync-assets
Section tags
1 shared · 4 only in A · 1 only in B- − test
- − lint-format
- − architecture
- − do-not
- + agent-behaviour
- code-style
Line diff
u9401066/zotero-keeper · .clinerules/50-pubmed-project.md
@@ −1 @@
1# PubMed Search MCP Project Rules
2
3These rules are meant for Cline usage in the PubMed Search MCP repository.
4
5## Goals
6
7- Provide a robust MCP server for biomedical literature search, analysis, full-text access, and citation export.
8- Make `unified_search` the default entrypoint while preserving specialized tools for PICO, MeSH, full text, citations, and pipelines.
9- Keep outputs useful for downstream agents and for Zotero Keeper imports.
10
11## Repo Layout
12
13- `src/pubmed_search/domain/`: domain entities and value objects.
14- `src/pubmed_search/application/`: search, export, pipeline, and analysis use cases.
15- `src/pubmed_search/infrastructure/`: external clients and source integrations.
16- `src/pubmed_search/presentation/mcp_server/`: MCP server, tools, prompts, and resources.
17- `tests/`: pytest suite.
18- `.claude/skills/`: user-facing research skills.
19- `.cline/skills/` and `.clinerules/`: Cline harness assets.
20
21## Canonical Commands
22
23- `uv run ruff check .`
24- `uv run ruff format --check .`
25- `uv run mypy src/ tests/`
26- `uv run pytest`
27- `uv run python scripts/count_mcp_tools.py --update-docs`
28- `python3 scripts/check_cline_skills.py`
29
30## Safety / Hygiene
31
32- Avoid editing generated outputs unless the generator was run intentionally.
33- Never commit NCBI API keys, Semantic Scholar keys, CORE keys, OpenAlex keys, cookies, or institutional resolver secrets.
34- Avoid destructive git operations unless explicitly requested.
35- Keep network-dependent behavior mockable and rate-limit aware.
36
37## Prefer Existing Patterns
38
39- Reuse source adapters and registry abstractions instead of adding one-off HTTP calls.
40- Keep MCP tools small and delegate behavior to application services.
41- Keep backward-compatible aliases where agents already consume fields.
42- Update tool docs and user-facing skills when tool contracts change.
43
u9401066/zotero-keeper · AGENTS.md
@@ +1 @@
1# Zotero + PubMed MCP Codex Harness
2
3These are the workspace instructions for Codex when using Zotero Keeper and
4PubMed Search MCP through the VS Code extension.
5
6## Goal
7
8Help the user search biomedical literature, inspect papers, and import selected
9articles into Zotero without losing provenance or overwriting user choices.
10
11## Working Style
12
13- Use Traditional Chinese unless the user asks otherwise.
14- Explain search/import steps briefly.
15- Ask before importing anything into Zotero.
16- Keep PubMed search/discovery/export work in PubMed Search MCP.
17- Keep persistence, collection selection, and Zotero inspection in Zotero Keeper.
18
19## Core Workflow
20
211. Start broad literature discovery with `unified_search`.
222. Use `parse_pico` and `generate_search_queries` for clinical or comparison questions.
233. Reuse session state with `get_session_pmids`, `get_cached_article`, and `get_session_summary`.
244. Use related/citing/reference/fulltext tools for follow-up instead of rerunning the same search.
255. Before saving to Zotero, call `list_collections` unless the destination is already confirmed.
266. Check duplicates with `check_articles_owned`.
277. Use `import_articles` as the default PubMed-to-Zotero handoff.
28
29## Repository Work
30
31- Treat `.codex/skills`, `.claude/skills`, `.cline/skills`, and `.clinerules` as bundled assistant harness assets.
32- Run `npm run sync-assets` before packaging the VSIX.
33- Keep `vscode-extension/resources/repo-assets/**` synchronized with its source files.
34- Preserve custom user `AGENTS.md`, Copilot instructions, and Cline settings during extension install/update flows.
35
36## Guardrails
37
38- Do not import into the Zotero root collection without explicit confirmation.
39- Do not assume the target collection.
40- Do not repeat searches when session state already contains the relevant PMIDs.
41- Distinguish peer-reviewed articles, preprints, and metadata-only records.
42- Keep NCBI email/API-key and institutional access settings intact.
43
44## Related Files
45
46- `.codex/skills/zotero-keeper-harness/SKILL.md`
47- `.codex/skills/pubmed-search-mcp-harness/SKILL.md`
48- `.github/zotero-research-workflow.md`
49- `.github/agents/research.agent.md`
50- `.claude/skills/pubmed-*`
51
@@ −1 +1 @@
1−# PubMed Search MCP Project Rules
1+# Zotero + PubMed MCP Codex Harness
22
3−These rules are meant for Cline usage in the PubMed Search MCP repository.
3+These are the workspace instructions for Codex when using Zotero Keeper and
4+PubMed Search MCP through the VS Code extension.
45
5−## Goals
6+## Goal
67
7−- Provide a robust MCP server for biomedical literature search, analysis, full-text access, and citation export.
8−- Make `unified_search` the default entrypoint while preserving specialized tools for PICO, MeSH, full text, citations, and pipelines.
9−- Keep outputs useful for downstream agents and for Zotero Keeper imports.
8+Help the user search biomedical literature, inspect papers, and import selected
9+articles into Zotero without losing provenance or overwriting user choices.
1010
11−## Repo Layout
11+## Working Style
1212
13−- `src/pubmed_search/domain/`: domain entities and value objects.
14−- `src/pubmed_search/application/`: search, export, pipeline, and analysis use cases.
15−- `src/pubmed_search/infrastructure/`: external clients and source integrations.
16−- `src/pubmed_search/presentation/mcp_server/`: MCP server, tools, prompts, and resources.
17−- `tests/`: pytest suite.
18−- `.claude/skills/`: user-facing research skills.
19−- `.cline/skills/` and `.clinerules/`: Cline harness assets.
13+- Use Traditional Chinese unless the user asks otherwise.
14+- Explain search/import steps briefly.
15+- Ask before importing anything into Zotero.
16+- Keep PubMed search/discovery/export work in PubMed Search MCP.
17+- Keep persistence, collection selection, and Zotero inspection in Zotero Keeper.
2018
21−## Canonical Commands
19+## Core Workflow
2220
23−- `uv run ruff check .`
24−- `uv run ruff format --check .`
25−- `uv run mypy src/ tests/`
26−- `uv run pytest`
27−- `uv run python scripts/count_mcp_tools.py --update-docs`
28−- `python3 scripts/check_cline_skills.py`
21+1. Start broad literature discovery with `unified_search`.
22+2. Use `parse_pico` and `generate_search_queries` for clinical or comparison questions.
23+3. Reuse session state with `get_session_pmids`, `get_cached_article`, and `get_session_summary`.
24+4. Use related/citing/reference/fulltext tools for follow-up instead of rerunning the same search.
25+5. Before saving to Zotero, call `list_collections` unless the destination is already confirmed.
26+6. Check duplicates with `check_articles_owned`.
27+7. Use `import_articles` as the default PubMed-to-Zotero handoff.
2928
30−## Safety / Hygiene
29+## Repository Work
3130
32−- Avoid editing generated outputs unless the generator was run intentionally.
33−- Never commit NCBI API keys, Semantic Scholar keys, CORE keys, OpenAlex keys, cookies, or institutional resolver secrets.
34−- Avoid destructive git operations unless explicitly requested.
35−- Keep network-dependent behavior mockable and rate-limit aware.
31+- Treat `.codex/skills`, `.claude/skills`, `.cline/skills`, and `.clinerules` as bundled assistant harness assets.
32+- Run `npm run sync-assets` before packaging the VSIX.
33+- Keep `vscode-extension/resources/repo-assets/**` synchronized with its source files.
34+- Preserve custom user `AGENTS.md`, Copilot instructions, and Cline settings during extension install/update flows.
3635
37−## Prefer Existing Patterns
36+## Guardrails
3837
39−- Reuse source adapters and registry abstractions instead of adding one-off HTTP calls.
40−- Keep MCP tools small and delegate behavior to application services.
41−- Keep backward-compatible aliases where agents already consume fields.
42−- Update tool docs and user-facing skills when tool contracts change.
38+- Do not import into the Zotero root collection without explicit confirmation.
39+- Do not assume the target collection.
40+- Do not repeat searches when session state already contains the relevant PMIDs.
41+- Distinguish peer-reviewed articles, preprints, and metadata-only records.
42+- Keep NCBI email/API-key and institutional access settings intact.
43+
44+## Related Files
45+
46+- `.codex/skills/zotero-keeper-harness/SKILL.md`
47+- `.codex/skills/pubmed-search-mcp-harness/SKILL.md`
48+- `.github/zotero-research-workflow.md`
49+- `.github/agents/research.agent.md`
50+- `.claude/skills/pubmed-*`
4351
