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* Fix upgrade-overwrites-copilot-skills: pass force=True to extension skill re-registration after upgrade Apply the remediation from the bug assessment on issue #3849. _register_extension_skills() had a skip guard that refused to overwrite existing SKILL.md files (protecting user customizations). In the upgrade path, setup() regenerates all core-template SKILL.md files first, then calls register_enabled_extensions_for_agent(). The guard then sees those freshly-written core files as 'existing' and skips every extension, leaving only core template content on disk. Fix: add force: bool = False to _register_extension_skills() and thread it through register_enabled_extensions_for_agent() and _register_extensions_for_agent(). In integration_upgrade(), pass force=True so extension content layers on top of the just-regenerated core files. The force flag is off-by-default so plain extension add still protects user-modified skill files. Refs #3849 Assisted-by: GitHub Copilot (model: claude-sonnet-4.6, autonomous) Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com> * Potential fix for pull request finding 'Unused local variable' Co-authored-by: Copilot Autofix powered by AI <223894421+github-code-quality[bot]@users.noreply.github.com> * test: add end-to-end regression guard for upgrade-overwrites-copilot-skills (#3849) The existing regression tests in TestRegisterExtensionSkillsForceFlag exercise the new force parameter at the helper level, so without the fix they fail only with a TypeError (unknown kwarg) rather than on the user-facing behaviour. Add a command-level test that runs 'specify integration upgrade copilot --skills --force' end-to-end and asserts the installed git extension's SKILL.md is restored (with its extension content, not a bare core-template stub) when the skill directory already exists — the exact skill_dir_preexists path the bug depends on. The test fails on pre-fix source (the skill is never recreated) and passes with the fix, so it is a genuine behavioural regression guard rather than an API-surface check. Refs #3849 Assisted-by: GitHub Copilot (model: claude-opus-4.8, autonomous) --------- Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com> Co-authored-by: Manfred Riem <15701806+mnriem@users.noreply.github.com> Co-authored-by: Copilot Autofix powered by AI <223894421+github-code-quality[bot]@users.noreply.github.com>