update-package-instructions

# update-package-instructions Update existing `.github/instructions/` files when an R/Bioconductor package changes, preserving manual customizations. ## Usage Invoke this skill when your package has changed and you want to refresh the AI instructions: - "Update the package instructions" - "Sync instructions with current package state" ## Prerequisites - Working directory is an R package root. - Existing instructions exist at `.github/instructions/`. ## Process 1. **Analyze Current State**: Run the `analyze-r-package` skill to produce a current package analysis. 2. **Identify Changes**: Read existing `.github/instructions/` `.md` files. Compare the current package analysis to the documented state to identify changes in metadata (version, dependencies), structure (functions, vignettes, classes), and content (data sources). 3. **Determine Update Scope**: Check which template variables have changed by referencing `templates/package-instructions/README.md`. If a variable differs, its corresponding file needs an update. 4. **Apply Update Strategy**: - **Preserve Custom Content**: Retain manually-added domain explanations, examples, and warnings. - **Update Systematically**: Update version numbers globally. Add new functions (with `[Description needed]`), remove deleted ones, and preserve custom descriptions. - **Targeted Edits**: Modify only the changed variables, rather than completely replacing files. 5. **Provide Update Summary**: Report the detected changes, updated files, and any items requiring manual review. ## Error Handling - **No instructions found**: Direct the user to `create-package-instructions`. - **Conflicts**: Prompt for a keep/replace/merge decision if manual changes conflict directly with template updates. ## Integration - **Uses**: `analyze-r-package` - **Works with**: `create-package-instructions` --- **Related**: See [create-package-instructions](../create-package-instructions/SKILL.md), [analyze-r-package](../analyze-r-package/SKILL.md).