Preserve global skill tracking across agents in unregister_agent_artifacts

The present-directory branch of ExtensionManager.unregister_agent_artifacts()
recomputed "remaining" registered_skills only by checking whether each name
still existed under the just-cleaned agent's own directory. registered_skills
is a single flat list shared across every agent an extension was ever
activated under (skills are only ever rendered for the currently active
agent, so there's no per-agent registry key). Repro: auggie and copilot both
have mirrors for the same extension; unregister_agent_artifacts("auggie")
correctly removes auggie's own mirror, sees the names absent from auggie's
(now empty) directory, and stores an empty registered_skills list - even
though copilot's mirror is still live on disk and now untracked. A later full
remove() then reads an empty registry and leaves copilot's mirror orphaned.

Fix: after the agent-scoped cleanup, recompute remaining names with
_extension_owned_skill_names(), which scans every safe, configured agent
skills directory (not just the one just cleaned) and keeps a name only if a
marker-verified SKILL.md for this extension still exists somewhere. This is
the same helper already used for the analogous same-agent toggle-cleanup
case, so no new abstraction was introduced. Explicit per-agent cleanup,
marker ownership verification, and symlink/containment safety are unchanged.

Added regression test:
- test_unregister_agent_artifacts_preserves_tracking_for_other_agent_mirror

Assisted-by: GitHub Copilot (model: Claude Sonnet 5, autonomous)
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

src/specify_cli/extensions/__init__.py

@@ -1901,15 +1901,21 @@ class ExtensionManager:
                 # When the directory does exist, _unregister_extension_skills
                 # may intentionally skip deletion when ownership cannot be
                 # verified (e.g., corrupted/missing SKILL.md or mismatching
-                # metadata.source). Only drop registry entries for skill
-                # directories that were actually removed so future cleanup
-                # attempts can still find skipped ones.
+                # metadata.source). A name no longer present under *this*
+                # agent's directory isn't necessarily gone everywhere either
+                # — registered_skills is a single flat list shared across
+                # every agent this extension was ever activated under, so
+                # an earlier activation under a different, still-active
+                # agent may have left its own marker-verified mirror behind.
+                # Recompute across every safe, supported skills directory
+                # (the same helper used for the analogous toggle-cleanup
+                # case) rather than just this one, or a still-existing
+                # mirror elsewhere would be silently dropped from tracking
+                # and orphaned on later removal (#2948).
                 if agent_skills_dir.is_dir():
-                    remaining_skills = [
-                        skill_name
-                        for skill_name in registered_skills
-                        if (agent_skills_dir / skill_name).is_dir()
-                    ]
+                    remaining_skills = self._extension_owned_skill_names(
+                        registered_skills, ext_id
+                    )
                     if remaining_skills != registered_skills:
                         updates["registered_skills"] = remaining_skills