`specify integration use copilot` against a Copilot install configured with
`--integration-options "--skills"` dropped `"ai_skills": true` from
init-options.json and regenerated extension commands in the legacy
`.agent.md`/`.prompt.md` layout, contradicting `integration.json`'s stored
`parsed_options.skills: true`.
`_update_init_options_for_integration` only inspected `SkillsIntegration` /
the instance `_skills_mode` flag. On the `use` path no `setup()` runs, so the
freshly-resolved Copilot instance has `_skills_mode == False` and the stored
skills intent in `parsed_options` was ignored. Thread the resolved
`parsed_options` through and treat `parsed_options["skills"]` as skills mode.
Adds a regression test that resets the registry singleton's `_skills_mode` to
simulate a fresh process (in-process singleton reuse otherwise masks the bug).
Assisted-by: GitHub Copilot (model: Claude Opus 4.8, autonomous)
Copilot-Session: 06fb6ae9-f444-4dfd-ab3f-d0669c5d0604
Co-authored-by: Copilot App <223556219+Copilot@users.noreply.github.com>
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