fix(presets): restore core skills instead of deleting them on preset remove (#3929)

* fix(presets): restore core skills instead of deleting them on preset remove

Skill restoration looked for core command templates under
.specify/templates/commands, a directory specify init never populates
in real projects. Since that lookup always missed, presets overriding
a core command (e.g. speckit.plan) had their skill deleted outright on
removal instead of restored — the actual core templates live in the
bundled core_pack (wheel install) or the repo-root templates/ tree.

Restoration now falls back to that bundled location, gated behind a
restore_from_bundled_core flag so the existing "retire a stale skill
superseded by a command-mode winner" path keeps deleting rather than
resurrecting a duplicate skill.

Fixes #3928

* fix(tests): use explicit utf-8 encoding reading restored skill content

read_text() defaults to the platform locale encoding, which is cp1252
("charmap") on Windows. The bundled specify.md core template contains a
UTF-8 multi-byte emoji whose bytes aren't valid cp1252, so the Windows CI
job failed decoding the restored SKILL.md with UnicodeDecodeError.

* fix(presets): keep extension restore priority over bundled-core fallback

The bundled-core fallback added for #3928 ran before the
extension_restore_index lookup, so a skill an installed extension owns
could be silently replaced by lower-priority bundled core content on
preset removal instead of preserving the extension's winning layer.

src/specify_cli/presets/__init__.py

@@ -2186,7 +2186,10 @@ class PresetManager:
             ]
             if dir_core_ext_names:
                 self._unregister_skills_in_dir(
-                    dir_core_ext_names, skills_dir, dir_agent
+                    dir_core_ext_names,
+                    skills_dir,
+                    dir_agent,
+                    restore_from_bundled_core=True,
                 )
 
             for _skill_name, cmd_name, top_layer in override_skills:
@@ -3021,6 +3024,7 @@ class PresetManager:
         preset_dir: Union[Path, str],
         *,
         additional_owned_sources: Optional[Dict[str, str]] = None,
+        restore_from_bundled_core: bool = False,
     ) -> Dict[Path, tuple[Optional[str], List[str]]]:
         """Restore original SKILL.md files after a preset is removed.
 
@@ -3028,6 +3032,17 @@ class PresetManager:
         regenerate the skill from the core command template.  If no core
         template exists, the skill directory is removed.
 
+        Args:
+            restore_from_bundled_core: When True, a missing project-local
+                core template (the common case — ``specify init`` never
+                populates ``.specify/templates/commands``) falls back to
+                the bundled core_pack/repo-root templates so the skill is
+                restored instead of deleted (#3928). Callers that are
+                retiring a skill because its command now renders elsewhere
+                (a command file superseding it) must leave this False so
+                the skill is removed rather than resurrected with core
+                content that would duplicate the winning command.
+
         ``registered_skills`` records exactly which agent directories this
         preset actually wrote to (see :meth:`_register_skills`), so removal
         restores precisely those directories rather than guessing at every
@@ -3101,6 +3116,7 @@ class PresetManager:
                     renderer_agent,
                     pack_id=pack_id,
                     additional_owned_sources=additional_owned_sources,
+                    restore_from_bundled_core=restore_from_bundled_core,
                 )
                 if mutated_names:
                     restored[skills_dir] = (
@@ -3133,6 +3149,7 @@ class PresetManager:
             selected_ai,
             pack_id=pack_id,
             additional_owned_sources=additional_owned_sources,
+            restore_from_bundled_core=restore_from_bundled_core,
         )
         return (
             {skills_dir: (selected_ai, mutated_names)}
@@ -3206,6 +3223,7 @@ class PresetManager:
         *,
         pack_id: Optional[str] = None,
         additional_owned_sources: Optional[Dict[str, str]] = None,
+        restore_from_bundled_core: bool = False,
     ) -> List[str]:
         """Restore original SKILL.md files within a single skills directory.
 
@@ -3216,6 +3234,7 @@ class PresetManager:
                 placeholder resolution and argument-hint formatting.
             additional_owned_sources: Generated non-preset source markers
                 accepted as owned for specific skill names.
+            restore_from_bundled_core: See ``_unregister_skills``.
 
         Returns:
             Skill names whose files were restored or removed.
@@ -3291,9 +3310,34 @@ class PresetManager:
                 if current_source not in owned_sources:
                     continue
 
-            # Try to find the core command template
-            core_file = core_templates_dir / f"{short_name}.md" if core_templates_dir.exists() else None
-            if core_file and not core_file.exists():
+            extension_restore = extension_restore_index.get(skill_name)
+
+            # Try to find the core command template. Project-local overrides
+            # in core_templates_dir take precedence, but that directory is
+            # rarely populated — the real core commands ship in the bundled
+            # core_pack (wheel install) or the repo-root templates/ tree
+            # (source checkout). Callers that want a genuine restore (a
+            # preset was removed outright, not superseded by another
+            # renderer) opt into that fallback via restore_from_bundled_core
+            # so the skill is restored instead of deleted (#3928). An
+            # installed extension providing a core-named command resolves
+            # ahead of bundled core elsewhere, so skip the bundled fallback
+            # when an extension restore exists — otherwise it would win
+            # over the higher-priority extension layer below.
+            core_file = core_templates_dir / f"{short_name}.md"
+            if (
+                not core_file.exists()
+                and restore_from_bundled_core
+                and extension_restore is None
+            ):
+                from .. import _locate_core_pack, _repo_root
+
+                _core_pack = _locate_core_pack()
+                if _core_pack is not None:
+                    core_file = _core_pack / "commands" / f"{short_name}.md"
+                else:
+                    core_file = _repo_root() / "templates" / "commands" / f"{short_name}.md"
+            if not core_file.exists():
                 core_file = None
 
             if core_file:
@@ -3338,7 +3382,6 @@ class PresetManager:
                 mutated_names.append(skill_name)
                 continue
 
-            extension_restore = extension_restore_index.get(skill_name)
             if extension_restore:
                 content = extension_restore["source_file"].read_text(encoding="utf-8")
                 frontmatter, body = registrar.parse_frontmatter(content)
@@ -3477,7 +3520,9 @@ class PresetManager:
                 "registered_skills", registered_skills
             )
             if persisted_skills:
-                self._unregister_skills(persisted_skills, dest_dir)
+                self._unregister_skills(
+                    persisted_skills, dest_dir, restore_from_bundled_core=True
+                )
             try:
                 if dest_dir.exists():
                     shutil.rmtree(dest_dir)
@@ -3815,6 +3860,7 @@ class PresetManager:
                 restorable_skills,
                 pack_dir,
                 additional_owned_sources=override_sources,
+                restore_from_bundled_core=True,
             )
             try:
                 from ..agents import CommandRegistrar