- Fix init --preset error masking: distinguish "not found" from real errors
- Fix bash resolve_template: skip hidden dirs in extensions (match Python/PS)
- Fix temp dir leaks in tests: use temp_dir fixture instead of mkdtemp
- Fix self-test catalog entry: add note that it's local-only (no download_url)
- Fix Windows path issue in resolve_with_source: use Path.relative_to()
- Fix skill restore path: use project's .specify/templates/commands/ not source tree
- Add encoding="utf-8" to all file read/write in agents.py
- Update test to set up core command templates for skill restoration
- Remove extraneous f-prefix from two f-strings without placeholders
- Replace substring URL check in test with startswith/endswith assertions
to satisfy CodeQL incomplete URL substring sanitization rule
- Add save_init_options() / load_init_options() helpers that persist
CLI flags from 'specify init' to .specify/init-options.json
- PresetManager._register_skills() overwrites SKILL.md files when
--ai-skills was used during init and corresponding skill dirs exist
- PresetManager._unregister_skills() restores core template content
on preset removal
- registered_skills stored in preset registry metadata
- 8 new tests covering skill override, skip conditions, and restore
