Detect locally modified skills and warn users during install

[mrsimpson]

Summary

This PR adds detection for locally modified inline skills and prevents them from being overwritten during install/setup operations. Users are now warned when their local skill modifications would be lost, with instructions on how to update them if desired.

Key Changes

• Modified writeInlineSkills() function to return a list of skill names that have been locally modified, instead of void

  • Now reads existing skill files before writing to detect changes
  • Skips writing files that have been locally modified
  • Only creates directories and writes files for new or unchanged skills

• Updated install and setup commands to handle modified skills

  • Both runInstall() and runSetup() now call writeInlineSkills() and check for modifications
  • Display a warning message listing any locally modified skills
  • Provide guidance to users on how to update skills if needed

• Refactored skill writing responsibility

  • Removed writeInlineSkills() call from claudeCodeWriter
  • Moved to CLI commands (install.ts and setup.ts) where it's called before installSkills()
  • Exported writeInlineSkills from harnesses package for use in CLI

Implementation Details

• The function now compares the expected skill content with existing file content before writing
• If content matches, the file is skipped (not added to modified list)
• If content differs or file doesn't exist, it's written normally
• Modified skills are collected and returned to the caller for user notification

https://claude.ai/code/session_01Sf3uGYRodvenEj8NWyzVcM