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[Idea] Add Ability for ai refresh to Skip Changes to AGENTS.md #79

Description

@homestar9

Summary

Executing coldbox ai refresh is the best way right now to make sure the .agents/manifest.json file gets updated with any custom skills developers add to the .agents/skills-custom/ folder. Unfortunately it also overwrites the root AGENTS.md file with the default.

Most developers are going to likely overwrite or heavily modify the AGENTS.md file with their particular project specs and instructions. Re-adding the ~300 lines of boilerplate on every refresh is inconvenient, and if missed, would add additional context to every chat that the developer may not want in there.

Possible Implementation Ideas

  1. If an AGENTS.md exists, but is missing the <!-- COLDBOX-CLI:START --> it would would not make changes to the file.
  2. Add an optional --noagents flag to the ai refresh command so the refresh won't touch the AGENTS.md file.
  3. Add an optional --manifest flag so the update will only update the skills/manifest stuff.
  4. Add a new CLI command ai refresh manifest to refresh just the manifest.

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