fix(presets): restore core skills instead of deleting them on preset remove

[chelsealong]

Fixes #3928

Bug

When a preset that overrides core commands/skills is removed, the corresponding
core skills are deleted instead of being restored — the only way to get them
back is to re-scaffold with specify init.

Root cause

PresetManager._unregister_skills_in_dir looks for the original core command
template at self.project_root / ".specify" / "templates" / "commands". That
directory is never populated by specify init in a real project — the actual
core command templates live in the bundled core_pack/commands/ directory
(wheel install) or the repo-root templates/commands/ tree (source checkout),
exactly like PresetResolver.resolve_core() already falls back to via
_locate_core_pack() / _repo_root().

Because the lookup always missed, every preset-removal restoration fell
through to the "no core template found" branch and deleted the skill outright.

Fix

Restoration now falls back to the bundled core_pack/repo-root templates when
the project-local override directory doesn't have the file. This fallback is
gated behind a new restore_from_bundled_core flag so the pre-existing "retire
a stale skill because its command now renders as a command file elsewhere"
path (triggered by ai_skills mode toggles) keeps its original delete
behavior — it must not resurrect a duplicate skill that a command file has
already superseded.

Repro (before the fix)

specify init --here --integration claude
specify preset add lean --dev presets/lean
ls .claude/skills          # all 10 core skills present
specify preset remove lean
ls .claude/skills          # only 5 remain — specify/plan/tasks/implement/constitution deleted

After the fix, all 10 skills are present again, restored with core content
after specify preset remove lean.

Testing

Added test_skill_restored_on_preset_remove_without_project_core_templates,
which (unlike the existing test_skill_restored_on_preset_remove) does not
pre-seed .specify/templates/commands with a fake core file, matching what a
real specify init project looks like. Confirmed it fails without the fix
(AssertionError: Core skill must be restored, not deleted) via
git checkout HEAD~1 -- src/specify_cli/presets/__init__.py, then passes with
the fix restored.

$ .venv/bin/python -m pytest tests/test_presets.py -q
526 passed in 7.40s

$ .venv/bin/python -m pytest tests -q
6380 passed, 9 skipped in 396.25s

$ .venv/bin/python -m pytest tests/test_agent_config_consistency.py -q
28 passed in 0.24s

$ uvx ruff@0.15.0 check src tests
All checks passed!

AI disclosure

This PR was authored primarily by an AI coding agent (Claude Code): it
diagnosed the root cause, implemented the fix, and wrote/verified the
regression test. I reviewed the diff and test output before submitting.

[Copilot]

Pull request overview

Fixes preset removal so overridden core skills are restored from bundled templates.

Changes:

• Adds opt-in bundled-core restoration for preset cleanup paths.
• Adds regression coverage for projects without local core command templates.

Show a summary per file

File	Description
src/specify_cli/presets/__init__.py	Adds bundled-core skill restoration fallback.
tests/test_presets.py	Tests restoration without local templates.

Review details

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• Files reviewed: 2/2 changed files
• Comments generated: 1
• Review effort level: Balanced

[chelsealong]

Fixed the Windows CI failure: the new test read the restored SKILL.md with read_text() (no explicit encoding), which defaults to the platform locale encoding — cp1252 ("charmap") on Windows. The bundled specify.md template contains a UTF-8 emoji whose bytes aren't valid cp1252, causing UnicodeDecodeError on windows-latest. Now reads with encoding="utf-8", matching how the file is written. Full suite (6380 passed, 9 skipped) and ruff pass locally.

[Copilot]

Review details

• Files reviewed: 2/2 changed files
• Comments generated: 0 new
• Review effort level: Balanced

[chelsealong]

Addressed the inline review comment: the bundled-core fallback now skips itself when extension_restore_index already has an entry for the skill, so an extension-owned skill restores from the extension rather than being replaced by lower-priority bundled core content. Added test_extension_wins_over_bundled_core_on_preset_remove (stubs the restore index since the extension command-namespace rules make a genuine end-to-end name collision hard to construct through real manifests); confirmed it fails without the fix. Full suite: 6381 passed, 9 skipped; ruff check src tests: all checks passed.

[Copilot]

Review details

• Files reviewed: 2/2 changed files
• Comments generated: 0 new
• Review effort level: Balanced

[mnriem]

Thank you!