Fix coldbox ai refresh custom-skill manifest crash and preserve AGENTS.md content outside managed markers

[Copilot]

coldbox ai refresh could crash when syncing skills-custom due to invalid closure scope usage in SkillManager. It could also overwrite user-authored AGENTS.md content when the managed marker block was repositioned.

• Custom skill sync crash fix (SkillManager.refresh)

  • Replaced closure access of arguments.manifest with the locally scoped manifest struct during custom-skill removal/sync.
  • Eliminates Lucee runtime errors when iterating skills-custom entries.

• Agent file merge hardening (AgentRegistry.mergeUserContent)

  • Updated merge logic to preserve user-authored content on both sides of the managed marker block:
    • content before<!-- COLDBOX-CLI:START -->
    • content after<!-- COLDBOX-CLI:END -->
  • Refresh now replaces only the managed section when a valid marker pair exists.

• Behavioral impact

  • coldbox ai refresh now safely picks up new/deleted custom skills without manifest-scope exceptions.
  • User-customized AGENTS.md remains intact outside the CLI-managed section, even if the marker block is moved lower in the file.

// before (inside closure): invalid in Lucee closure scope
var alreadyInManifest = !arguments.manifest.customSkills
.filter( ( s ) => s.name == dirName )
.isEmpty()
// after: uses surrounding function scope safely
var alreadyInManifest = !manifest.customSkills
.filter( ( s ) => s.name == dirName )
.isEmpty()

[Copilot]

Pull request overview

This PR improves the reliability of coldbox ai refresh by fixing a Lucee closure-scope crash during custom-skill syncing and by hardening the agent file merge logic to preserve user-authored content outside the CLI-managed marker block.

Changes:

• Fixes Lucee closure scoping in SkillManager.refresh() by using the function-scoped manifest reference inside each()/filter() closures.
• Updates AgentRegistry.mergeUserContent() to preserve content both before <!-- COLDBOX-CLI:START --> and after <!-- COLDBOX-CLI:END --> when refreshing agent files.
• Updates inline documentation to reflect the new marker-pair behavior.

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 1 comment.

File	Description
models/SkillManager.cfc	Uses function-scoped manifest inside closures to prevent Lucee runtime errors when syncing/removing skills-custom entries.
models/AgentRegistry.cfc	Reworks merge logic to preserve user content on both sides of the managed marker block during refresh.

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