[Bug]: Core skills get deleted when preset is removed

[nicolehaugen]

Bug Description

When you remove a preset that override's core commands/skills, the corresponding .github/skills files are deleted - instead, core's skills should still be retained.

Steps to Reproduce

Repro:

1.) Add pirate speak preset that overrides all the core's commands (for example use the /speckit-preset plugin and prompt to add the preset)
2.) Open the .github\skills folder for your project, and validate the pirate speak skills that are generated
3.) Remove the pirate speak preset (for example use the /speckit-preset plugin and prompt to remove it)
4.) Look at the contents of the .github\skills folder again:

• Expected - All of the core skills should still exist
• Actual - All of the core skills are deleted with removing the pirate speak preset

It seems the only way to fix this is to use project init again, to rescaffold the core skills which isn't desirable.

Expected Behavior

All core skills should still be retained.

Actual Behavior

All core skills get deleted

Specify CLI Version

0.15.0

AI Agent

GitHub Copilot

Operating System

Windows 11

Python Version

3.12.10

Error Logs

Additional Context

No response

[nicolehaugen]

Note analysis from copilot:

What the code actually does on preset remove
Looking at src/specify_cli/presets/init.py, the removal path calls _unregister_commands and _delete_agent_preset_skills for exactly the commands the preset registered (tracked in registered_commands / registered_skills). It's not supposed to touch anything the preset didn't register.
BUT — the critical detail I missed earlier: for native skills-mode agents (extension: "/SKILL.md"), preset overrides are materialized in place over the core skill files. When you remove the preset, the code calls _delete_agent_preset_skills on those file paths — and the comment says it's a plain delete, not a "restore from core."
That comment (line 1414–1420) explicitly flags the risk:
"unregistering through both paths would double-process the identical directory (delete via the commands path, then no-op 'restore' via the skills path since the directory is already gone)"
So the removal path deletes the skill directory and relies on some other mechanism to re-scaffold core. If that re-scaffold doesn't run — or is broken for a full-workflow-replacement preset like your Pirate Speak — you get exactly what you saw: all skills gone.