docs: explain load-bearing pre-create loop in _reconcile_skills

The per-skill _validate_skill_subdir(create=True) loop looks like dead
code (its result is unused), but it re-creates the tracked skill
subdirectories that _unregister_skills just deleted so
_register_skills's only-overwrite-existing gate passes during a
historical-directory restore. Removing it fails
test_skill_reconciliation_preserves_per_directory_names.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

Author: marcelsafin

src/specify_cli/presets/__init__.py

@@ -2219,6 +2219,14 @@ def apply_to_dir(
                     continue
                 cmds_set = set(dir_cmds)
                 filtered_manifest = self._FilteredManifest(manifest, cmds_set)
+                # Not dead code: _register_skills only *overwrites* skill
+                # subdirectories that already exist (plus brand-new ones for
+                # the active ai_skills agent). For a restore into a
+                # historical directory, _unregister_skills has just deleted
+                # the retiring preset's subdirectory, so pre-create the
+                # tracked (dir_managed_names) subdirectories here — under
+                # the same symlink guard — or the surviving preset's
+                # override would be silently skipped (#2948).
                 for cmd_name in dir_cmds:
                     for skill_name in self._skill_names_for_command(cmd_name):
                         if skill_name not in dir_managed_names: