Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[Unreleased]

CI/CD Skills Validation
- Added GitHub Actions workflow .github/workflows/validate-skills.yml to run structural validation automatically on PRs.
- Added deterministic check script scripts/validate_skills.py to enforce required frontmatter fields, name matching, uniqueness, link integrity, and version bumps.
- Added .github/copilot-instructions.md to guide GitHub Copilot Code Review for inline subjective feedback on PRs.
Bioc-HowTo Integration
- Merged waldronlab/ai-agent-skills into the official bioconductor/ai-agent-skills repository.
- Added bioc-howto skill and 11 R-oriented how-to guides (e.g. coverage computation, sequence composition, GRanges manipulation, BAM reading).
GitHub Pages Navigation
- Improved documentation structure and FAQ accessibility on GitHub Pages.

validate-skill (v1.1.0 → v1.2.0) - Updated with CI/CD integration note clarifying the local vs CI/CD division of labor.
antigravity adapter (formerly gemini) - Updated setup instructions and renamed adapter to instructions/antigravity.md.

security-audit-r-package (v1.0.0) - Comprehensive security auditing for R/Bioconductor packages
- Analyzes R code, native code (C/C++/Fortran), dependencies, and package structure
- References external gist as single source of truth for security checks and issue labels
- Flexible output formatting (structured reports for full audits, concise for quick checks)
- Supports targeted audits (specific files/directories) or full package scope
AGENTS.md § Avoiding Content Duplication - Guidelines for preventing SSOT violations
SKILL_STANDARD.md § SSOT Compliance checklist

create-skill (v1.2.1 → v1.3.0) - Added comprehensive “Avoiding SSOT Violations” guidance
- SSOT = Single Source of Truth (avoid duplicating content across skills, documentation, validation)
- Lists what not to duplicate (YAML specs, validation criteria, external checklists)
- Provides reference patterns with examples
- Documents signs of SSOT violation and fix patterns
validate-skill (v1.0.1 → v1.1.0) - Added SSOT violation detection
- New validation step 8: “Check for SSOT Violations”
- Flags common duplication patterns (field lists, templates, copied checklists)
- Validates proper reference patterns
document-skill (v1.0.1) - Reduced duplication in YAML field descriptions

Meta skills now reference AGENTS.md as single source of truth (~95 lines of duplication removed)
All YAML field specifications reference AGENTS.md § Skill File Format
All validation criteria reference AGENTS.md § Minimal Required Fields / What NOT to Include
Validation report templates simplified (reduced from 76 lines to ~30 lines)
SKILL_STANDARD.md updated to v2.1.0 with SSOT compliance checklist

AGENTS.md - Canonical agent behavior standard
SKILL_STANDARD.md - Quick reference with checklist and examples
document-skill - Automates SKILLS.md updates after skill creation
validate-skill - Validates skills against repository standards
check-bioconductor-skills - Verifies installation and lists available skills
Complete r-packages skill suite (analyze-r-package, create-package-instructions, update-package-instructions)
instructions/ directory with platform adapters (claude.md, copilot.md, antigravity.md)
Migration guide in SKILL_STANDARD.md for v1.x users