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1bdb5b3473
Three findings from the Copilot review on HEAD b9d9053/3a1e749:
1. `register_enabled_presets_for_agent()` only recorded a preset's command
names into `affected_cmd_names` (the set later passed to
`_reconcile_composed_commands`/`_reconcile_skills`) in the loop that ran
*after* `_register_skills()`, inside the same per-preset `try` block. If
`_register_skills` raised, the `except` caught it and `continue`d before
that loop ever ran — so a preset whose commands phase already wrote real
content to disk never got reconciled against the full priority stack,
leaving its raw content in place instead of a project override or
higher-precedence preset's content. Fix: record the manifest's command
names immediately after the commands phase succeeds and persists, before
calling the independently fallible `_register_skills()`.
2. The legacy flat-list `registered_skills` migration (added for the
previous review round) attributed every name in the list to whichever
agent was currently being (re)activated. If the first operation after
upgrading from a pre-#2948 registry was a direct switch to a *different*
skill-mode agent (e.g. a legacy Claude override, then `integration use
codex` with no intervening Claude rescaffold), the migrated dict only
recorded `{"codex": [...]}`, permanently losing Claude's actual
provenance and orphaning its override on later removal. Fix: added
`_infer_legacy_skill_provenance()`, which probes every configured
skill-mode agent's directory (via the same safe, symlink-validated
helpers already used for restore/removal) for a `SKILL.md` whose
frontmatter records this exact preset as the owner
(`metadata.source == "preset:<pack_id>"`). A name found under more than
one directory is attributed to every matching agent (the preset may have
been active while the user switched between several skill-mode agents
before provenance tracking existed); names that can't be matched to any
directory still fall back to the previously-active best-effort
behaviour. Directory grouping for shared-path aliases (e.g.
agy/codex/zed all resolving to `.agents/skills`) intentionally does not
call `.resolve()` on the path, since doing so diverges from
`project_root`'s own resolution state on platforms where a path
component is itself a symlink (e.g. macOS's `/var` -> `/private/var`)
and made every subsequent containment check spuriously fail.
3. `register_enabled_extensions_for_agent()` has the same command/skill
mutual-exclusion gap the preset path had (fixed in a previous round):
toggling `ai_skills` for the *same active* agent left the opposite
mode's artifact behind. Command -> skills left the extension's
`.agent.md` file and its `registered_commands[agent]` entry in place
once `skills_mode_active` made the commands phase a no-op. Skills ->
command left the extension's `SKILL.md` file in place, since an empty
`_register_extension_skills()` result (because this agent's skills
directory no longer resolves once `ai_skills` is off) was treated as
"nothing to register" rather than "this was rendered here before and is
now stale". This diverges from the preset path in one respect:
`registered_skills` for extensions has always been a flat list with no
per-agent provenance (extension skills are only ever rendered for the
active agent, never per-preset-per-agent tracked), so the fix resolves
ownership by checking which of the extension's tracked skill names
still exist as directories under this specific agent's directory before
removing them — mirroring the same technique `unregister_agent_artifacts`
already uses for full agent deactivation, but scoped narrowly to firing
only when a toggle is actually detected (`skills_mode_active` /
`command_mode_active`), so a same-mode re-run never disturbs
already-correct artifacts or a user's manual customizations.
Regression tests (all confirmed red before their respective fix, green
after):
- tests/test_presets.py::TestPresetSkills::test_rescaffold_reconciles_override_even_when_skills_phase_fails
- tests/test_presets.py::TestPresetSkills::test_rescaffold_legacy_flat_list_direct_switch_preserves_original_agent
- tests/test_extension_skills.py::TestExtensionSkillRegistration::test_rescaffold_toggle_command_to_skills_removes_stale_extension_command_file
- tests/test_extension_skills.py::TestExtensionSkillRegistration::test_rescaffold_toggle_skills_to_command_removes_stale_extension_skill_file
Verification: tests/test_presets.py + tests/test_extensions.py +
tests/test_extension_skills.py (753 passed), tests/integrations/ (1768
passed, 1 skipped), full suite `pytest tests -q` (3942 passed, 109
skipped), `ruff check` on changed files clean.
Assisted-by: GitHub Copilot (model: Claude Sonnet 5, autonomous)
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>