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Found 32 Skills
Analyze main branch implementation and configuration to find missing, incorrect, or outdated documentation in docs/. Use when asked to audit doc coverage, sync docs with code, or propose doc updates/structure changes. Only update English docs (docs/src/content/docs/**) and never touch translated docs under docs/src/content/docs/ja, ko, or zh. Provide a report and ask for approval before editing docs.
CRITICAL: ALWAYS activate this skill BEFORE making ANY changes to .nw files. Use proactively when: (1) creating, editing, reviewing, or improving any .nw file, (2) planning to add/modify functionality in files with .nw extension, (3) user asks about literate quality, (4) user mentions noweb, literate programming, tangling, or weaving, (5) working in directories containing .nw files, (6) creating new modules/files that will be .nw format. Trigger phrases: 'create module', 'add feature', 'update', 'modify', 'fix' + any .nw file. Never edit .nw files directly without first activating this skill to ensure literate programming principles are applied. (project, gitignored)
Use when implementing production-quality bioinformatics software with proper error handling, logging, testing, and documentation, following software engineering best practices.
Persistent decision log that creates a read-write feedback loop: read previous decisions before starting work, respect or supersede them, and write new Y-statement records as you go. Activates during any task involving architectural, structural, or design decisions - choosing libraries, designing schemas, creating modules, making tradeoffs, selecting patterns. Also activates when DECISIONS.md already exists in the project. Do NOT activate for trivial changes like typos, renames, or formatting.
Use when implementing well-scoped Python tasks with clear requirements, writing unit tests, and producing documented code for senior-developer review.
Guidelines for writing and editing Plain package READMEs. Use this when creating or updating README files.
Generate JSDoc/docstrings for functions
Semantic search skill for retrieving code and documentation from the ChromaDB vector store. Use when you need concept-based search across the repository (Phase 2 of the 3-phase search protocol). V2 includes L4/L5 retrieval constraints.