update-package-instructions

name	update-package-instructions
description	Update existing AI instruction documentation when an R/Bioconductor package changes
version	1.0.0
category	r-packages
tags	["r-packages","documentation","bioconductor"]
author	waldronlab

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

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Related: See create-package-instructions, analyze-r-package.