Cline rules

1---
2paths:
3  - ".clinerules/workflows/llm-wiki-build.md"
4  - ".cline/skills/llm-wiki-builder/SKILL.md"
5  - ".codex/skills/llm-wiki-builder/SKILL.md"
6  - ".github/zotero-research-workflow.md"
7---
8 
9# Foam LLM Wiki Rules
10 
11Use these rules when turning Zotero, PubMed, PDF/full-text, or project evidence
12into a Foam-compatible Markdown wiki for LLM-assisted reading and synthesis.
13 
14## Asset Boundaries
15 
16- Treat Foam wiki files as user-authored knowledge assets, not generated trash.
17- Detect the wiki root before writing. Prefer an existing Foam workspace layout
18  such as `.foam/`, `.vscode/settings.json`, or an existing note graph.
19- Ask before bulk rewrites, renames, deletions, or moving an existing wiki root.
20- Keep raw exports, RIS, JSON, and tool responses out of final notes unless the
21  user explicitly asks for an appendix.
22 
23## Foam Rendering Invariants
24 
25- Create ordinary Markdown files that render without custom HTML.
26- Use one `# H1` title per note, matching the human-readable note title.
27- Use stable lowercase kebab-case filenames for new generated notes.
28- Put display titles and source identifiers in YAML frontmatter when useful.
29- Use Foam wikilinks only for real note targets:
30  - `[[note-slug]]` when the target note exists or is created in the same workflow.
31  - `[[note-slug|Readable label]]` when the filename is less readable than the title.
32- Use relative Markdown links for attachments, figures, PDFs, or exported files.
33- Do not leave unresolved wikilinks unless they are intentionally marked as TODO.
34 
35## Evidence And Citation Hygiene
36 
37- Preserve PMID, DOI, PMCID, Zotero key, URL, title, journal, year, and access
38  status whenever available.
39- Distinguish imported Zotero items, candidate PubMed results, and preprints.
40- Cite claims at paragraph or bullet level using compact source markers such as
41  `PMID:12345678`, `DOI:...`, or `Zotero:ABC123`.
42- Prefer exact text spans, section names, page numbers, or quote hashes when a
43  full-text or asset-aware tool provides them.
44- Do not claim that a note is citation-ready unless its source markers can be
45  traced back to a concrete article, item, or document span.
46 
47## Workflow And Skill Split
48 
49- Rules define durable wiki constraints and rendering invariants.
50- Workflows define the complete user-facing sequence for making or refreshing
51  an LLM wiki.
52- Skills orchestrate multiple tools: filesystem search, Zotero inspection,
53  PubMed discovery, full-text/asset extraction when available, Markdown writes,
54  and link validation.
55