fix(bob): restrict layout reconciliation to the active integration (review #3415)

`integration_upgrade` supports upgrading a secondary (non-active) integration,
but the layout-change extension reconciliation was unsafe there.
`ExtensionManager.unregister_agent_artifacts()` treats the unscoped
per-extension `registered_skills` list as belonging to the passed agent and,
when that agent's skills directory is absent, falls back to scanning every
agent's skills directory — so reconciling a secondary Bob layout flip could
delete or untrack the *active* agent's extension skills. The subsequent
re-registration cannot repair that because extension skill rendering is
intentionally scoped to the active agent (#2948).

Gate the unregister-before-register reconciliation on `installed_key == key`
so it only runs for the active integration. Secondary agents only ever have
extension command files (skills are active-agent-only), which the existing
re-registration rewrites in place, so skipping the unregister orphans nothing
new. Adds a regression test asserting a secondary Bob layout change leaves the
active agent's extension skill intact on disk and in the registry.

Assisted-by: GitHub Copilot (model: Claude Opus 4.8, autonomous)
Co-authored-by: Copilot App <223556219+Copilot@users.noreply.github.com>
Copilot-Session: 63f93544-a77f-4f01-bf04-c88806a97dbf

Author: mnriem

src/specify_cli/integrations/_migrate_commands.py

@@ -612,6 +612,19 @@ def integration_upgrade(
     # re-registration below recreates them in the new layout. ``upgrade``s that
     # don't change layout skip this to avoid needless remove/re-add churn.
     #
+    # Only the *active* integration is reconciled this way (``installed_key ==
+    # key``).  ``ExtensionManager.unregister_agent_artifacts`` treats the
+    # per-extension ``registered_skills`` list as belonging to the passed agent
+    # and, when that agent's skills directory is absent, falls back to scanning
+    # every agent's skills directory — so running it for a *secondary*
+    # (non-active) agent could delete or untrack the *active* agent's extension
+    # skills.  The subsequent re-registration cannot repair that because
+    # extension skill rendering is intentionally scoped to the active agent
+    # (#2948).  Extension skills only ever exist for the active agent, so
+    # skipping the unregister for a secondary agent orphans nothing new: a
+    # secondary agent only has extension *command* files, which the
+    # re-registration below rewrites in place regardless of layout.
+    #
     # Known limitation: preset command/skill artifacts are NOT reconciled on a
     # layout change. There is no agent-scoped preset re-registration mechanism
     # anywhere in the CLI — ``use`` / ``switch`` / ``upgrade`` never reconcile
@@ -622,8 +635,10 @@ def integration_upgrade(
     # layout) when no preset artifacts are at stake. Full preset reconciliation
     # would require a new cross-cutting PresetManager subsystem affecting every
     # dual-layout agent, which is out of scope for this Bob migration.
-    if _manifest_tracks_skill_layout(old_manifest) != _manifest_tracks_skill_layout(
-        new_manifest
+    if (
+        installed_key == key
+        and _manifest_tracks_skill_layout(old_manifest)
+        != _manifest_tracks_skill_layout(new_manifest)
     ):
         _unregister_extensions_for_agent(
             project_root,

tests/integrations/test_integration_subcommand.py

@@ -2662,6 +2662,63 @@ def test_upgrade_bob_layout_change_rejected_with_presets_installed(self, tmp_pat
             f"same-layout upgrade must not be blocked by presets: {result.output}"
         )
 
+    def test_upgrade_secondary_bob_layout_change_preserves_active_agent_skills(
+        self, tmp_path
+    ):
+        """Regression (review #3415, 4726347306).
+
+        ``integration upgrade`` supports upgrading a *secondary* (non-active)
+        integration. The layout-change extension reconciliation must NOT run
+        for a secondary agent: ``unregister_agent_artifacts`` treats the
+        unscoped per-extension ``registered_skills`` as belonging to the passed
+        agent and, if that agent's skills dir is absent, scans every agent's
+        skills dir — which could delete/untrack the *active* agent's extension
+        skills. The following re-registration cannot repair that because
+        extension skill rendering is active-agent-scoped (#2948).
+        """
+        # Active agent: copilot in skills mode → git extension renders as skills.
+        project = _init_project(tmp_path, "copilot", integration_options="--skills")
+        result = _run_in_project(project, ["extension", "add", "git"])
+        assert result.exit_code == 0, f"extension add failed: {result.output}"
+
+        skill = project / ".github" / "skills" / "speckit-git-feature" / "SKILL.md"
+        assert skill.exists(), "precondition: active copilot has the git extension skill"
+
+        registry_path = project / ".specify" / "extensions" / ".registry"
+
+        def _git_skills():
+            data = json.loads(registry_path.read_text(encoding="utf-8"))
+            return data["extensions"]["git"].get("registered_skills", [])
+
+        assert _git_skills(), "precondition: git skills registered for active copilot"
+
+        # Add a secondary (non-active) Bob in the legacy commands layout.
+        result = _run_in_project(project, [
+            "integration", "install", "bob",
+            "--integration-options", "--legacy-commands",
+            "--script", "sh", "--force",
+        ])
+        assert result.exit_code == 0, result.output
+
+        # Flip the *secondary* Bob's layout to skills. copilot stays active.
+        result = _run_in_project(project, [
+            "integration", "upgrade", "bob",
+            "--integration-options", "--skills",
+            "--script", "sh", "--force",
+        ])
+        assert result.exit_code == 0, result.output
+
+        # The active agent's extension skill must be untouched on disk and in
+        # the registry — the secondary layout change must not reconcile it.
+        assert skill.exists(), (
+            "secondary Bob layout change must not delete the active agent's "
+            "extension skill"
+        )
+        assert _git_skills(), (
+            "secondary Bob layout change must not untrack the active agent's "
+            "extension skills in the registry"
+        )
+
     def test_upgrade_preserves_existing_vscode_settings(self, tmp_path):
         """Regression: copilot upgrade must not stale-delete .vscode/settings.json.