fix(integrations): move extension artifacts on integration uninstall

[Chaoqi31]

Description

specify integration uninstall <agent> removes the integration's own files but leaves the extension and preset commands and skills registered for that agent. When the uninstalled integration was the default, it also promotes another integration without registering the enabled extensions and presets for it. use and switch both do these steps; uninstall did not. Reproduction with the bundled git extension:

$ specify init p1 --integration claude --ignore-agent-tools --non-interactive
$ cd p1 && specify integration install gemini
$ specify extension add git
$ specify integration uninstall claude
✓ Integration 'Claude Code' uninstalled
  Removed 10 file(s)
$ find .claude -type f
.claude/skills/speckit-git-commit/SKILL.md          # left behind, no integration owns .claude/ now
.claude/skills/speckit-git-feature/SKILL.md
... (five speckit-git-* skills)
$ find .gemini -type f | grep git
(nothing)                                           # the new default has no extension commands
$ specify integration use gemini && find .gemini -type f | grep git
.gemini/commands/speckit.git.commit.toml            # what uninstall should have done
... (five files)

Presets go the same way: with the bundled lean preset installed, uninstalling claude leaves five of its override skills in .claude/skills/, and gemini keeps the core commands instead of the preset's.

#4862 added these two steps for catalog-installed adapters only, inside the external_lifecycle wrapper. That wrapper returns before its transaction when no external adapter is involved, so built-in integrations never reached them. This PR does them in the uninstall command itself, for every integration and also on the "no manifest" path, using the same helpers (the fallback messages are the wrapper's; the cleanup messages follow switch). The wrapper now cleans up only the stale adapter records it removes alongside the uninstalled integration, and no longer registers the fallback, so external adapters do not run the steps twice. The integrations reference now describes the behaviour under Uninstall.

Behaviour notes: the extensions and presets stay installed; only the files registered for the removed agent go. As with switch, an extension command file the user edited is removed with its agent.

Testing

• New test_uninstall_unregisters_extension_and_preset_artifacts, with the bundled git extension and a dev preset that overrides speckit.specify: the extension skill, the preset skill and their registry entries are gone after uninstall. On main: Extension skill should be removed with its agent.
• New test_uninstall_default_registers_contributions_for_fallback, run with and without the integration manifest: the promoted default gets the extension skill and the preset override. On main: Promoted default should receive enabled extensions (both cases).
• New negative case test_uninstall_non_default_preserves_default_contributions: uninstalling a non-default integration leaves the default's extension and preset files and registry entries in place.
• With the preset calls taken out of the uninstall command, the first two tests fail on their preset assertions (Preset skill should be removed with its agent, Promoted default should receive enabled presets), so the preset steps are covered on their own.
• New test_uninstall_cleans_up_contributions_of_stale_adapter_record in test_installed_adapters.py: an external adapter whose record is no longer in integration.json is removed when another integration is uninstalled, and its extension and preset files and registry entries go with it. It passes on main and fails on this PR's first revision (535a397), which left .sample-agent/skills/speckit-git-commit/SKILL.md behind.
• test_command_uninstall.py with test_installed_adapters.py: 683 passed. tests/specify_cli, tests/integrations and tests/test_extensions.py: 7782 passed, 7 skipped.
• Reran the CLI steps above, and the same steps with the lean preset, against this branch: .claude/ holds no files afterwards, .gemini/commands/speckit.git.*.toml exist, and gemini's commands come from lean.

Equivalent local checks: tests ran with .venv/bin/python -m pytest and the CLI with the venv's specify, on macOS.

AI Disclosure

• I did not use AI assistance for this contribution
• I did use AI assistance (fill in the disclosure below)

AI disclosure: This contribution was produced by Claude Code running autonomously on behalf of @Chaoqi31. An audit agent (Claude Fable 5.1, max reasoning effort) found the bug and wrote a failing reproduction. A fix agent (Claude Opus 5, xhigh effort) wrote the fix, tests and docs sentence. A separate review agent (Claude Fable 5.1, max reasoning effort) checked the branch, and the orchestrating agent (Claude Opus 5) reran the CLI reproductions and wrote the commits and this description. Claude Code (Claude Opus 5) also wrote the follow-up commits for review feedback. AI generated the code, tests and text. No human reviewed the diff line by line before submission.

[Copilot]

🟡 Changes recommended

Package reconciliation can orphan stale-adapter contributions, and built-in preset behavior lacks required regression coverage.

2 open findings

• Preserve cleanup for all stale packages removed during reconciliation · New
• Add regression coverage for built-in preset cleanup and registration · New

What changed in this PR

Moves extension and preset artifact migration into the integration uninstall command for built-in and external integrations.

Changes:

• Cleans artifacts for uninstalled integrations.
• Registers artifacts for a promoted default integration.
• Adds extension regressions and updates uninstall documentation.

File	Description
command_uninstall.py	Handles artifact cleanup and fallback registration.
_lifecycle.py	Removes duplicate external-adapter handling.
test_command_uninstall.py	Adds extension uninstall regressions.
integrations.md	Documents uninstall behavior.

🧠 Review effort: Balanced

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[mnriem]

Please address Copilot feedback

[Copilot]

🟢 Approval recommended

The lifecycle changes are consistent with the integration design and include positive, negative, and regression coverage.

0 open findings

2 resolved since last review

• Preserve cleanup for all stale packages removed during reconciliation
• Add regression coverage for built-in preset cleanup and registration

🧠 Review effort: Balanced

[Chaoqi31]

@mnriem Both Copilot comments are addressed in 28df6e1 and bd65b28. Details are in the threads, and the description's Testing section is updated.

AI disclosure: Claude Code (Claude Opus 5), running autonomously for @Chaoqi31, wrote this change and this reply.

[mnriem]

Thank you!