fix: persist command registration before fallible skills phase on rescaffold

Fix remaining round-6 review findings on the active-only integration
registration work (#2948):

- register_enabled_presets_for_agent(): registered_commands and
  registered_skills were merged and persisted together in a single
  registry.update() call after both the commands and skills phases ran.
  If _register_skills() raised, the per-preset try/except swallowed it
  before that update() call was reached, even though _register_commands()
  had already written a real command file to disk. That file became
  untracked, so preset removal could no longer clean it up.
  install_from_directory() already persists registered_commands
  immediately after the commands phase, before starting the independently
  fallible skills phase; rescaffold now does the same.

- test_presets.py: renamed a misleading claude_dir variable (pointing at
  Gemini's command directory) in
  test_composed_none_unregister_respects_active_agent to reuse the
  existing gemini_commands_dir variable already defined earlier in the
  same test.

Added regression test
test_rescaffold_persists_commands_before_fallible_skills_phase:
simulates a skills-phase failure during rescaffold and asserts the
command file already written to disk is still tracked in
registered_commands.

Verified all other round-6 findings (preset active-integration scoping,
preset reconciliation/remove paths, skills-mode switching, override
precedence during rescaffold, skill-subdirectory symlink safety) are
already addressed by prior commits in this branch; re-checked each
against current code before concluding no further change was needed.

Targeted (tests/test_presets.py, tests/test_extensions.py: 689 passed)
and full (3935 passed, 109 skipped) suites and ruff check on changed
files pass clean.

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

src/specify_cli/presets/__init__.py

@@ -762,8 +762,6 @@ class PresetManager:
             # Isolate per-preset failures: one preset that fails to register
             # must not abort registration of the remaining enabled presets.
             try:
-                updates: Dict[str, Any] = {}
-
                 registered_commands = self._register_commands(manifest, pack_dir)
                 existing_commands = metadata.get("registered_commands", {})
                 if not isinstance(existing_commands, dict):
@@ -771,8 +769,13 @@ class PresetManager:
                 merged_commands = copy.deepcopy(existing_commands)
                 if registered_commands.get(agent_name):
                     merged_commands[agent_name] = registered_commands[agent_name]
+                # Persist the commands phase immediately, mirroring
+                # install_from_directory(): _register_skills is an
+                # independently fallible phase, and if it raises, the files
+                # the commands phase already wrote to disk must still be
+                # tracked so preset removal can clean them up (#2948).
                 if merged_commands != existing_commands:
-                    updates["registered_commands"] = merged_commands
+                    self.registry.update(pack_id, {"registered_commands": merged_commands})
 
                 registered_skills = self._register_skills(manifest, pack_dir)
                 existing_skills = self._normalize_registered_skills(
@@ -782,10 +785,7 @@ class PresetManager:
                 if registered_skills.get(agent_name):
                     merged_skills[agent_name] = registered_skills[agent_name]
                 if merged_skills != existing_skills:
-                    updates["registered_skills"] = merged_skills
-
-                if updates:
-                    self.registry.update(pack_id, updates)
+                    self.registry.update(pack_id, {"registered_skills": merged_skills})
 
                 for tmpl in manifest.templates:
                     if tmpl.get("type") == "command":