fix: recover active skills registration for extensions (#2803)

Extension command registration now resolves the active skills directory before writing command artifacts. This lets initialized skills-backed agents recover a missing active skills directory while preserving the existing preset registration behavior.

Add regression coverage for missing active skills directories, shared skills directories, and symlinked parent guards.

Fixes #2769.

Co-authored-by: OpenAI Codex <codex@openai.com>

src/specify_cli/extensions.py

@@ -26,14 +26,15 @@ from packaging import version as pkg_version
 from packaging.specifiers import SpecifierSet, InvalidSpecifier
 
 from .catalogs import CatalogEntry as BaseCatalogEntry, CatalogStackBase
+from ._init_options import is_ai_skills_enabled
 
 _FALLBACK_CORE_COMMAND_NAMES = frozenset({
     "analyze",
-    "checklist",
     "clarify",
     "constitution",
     "implement",
     "plan",
+    "checklist",
     "specify",
     "tasks",
     "taskstoissues",
@@ -830,15 +831,53 @@ class ExtensionManager:
         be created due to symlink, containment, or permission issues so
         that callers can fall back gracefully.
         """
-        from . import resolve_active_skills_dir, _print_cli_warning
+        from . import (
+            _print_cli_warning,
+            load_init_options,
+            resolve_active_skills_dir,
+        )
+
+        def _ensure_usable(skills_dir: Path) -> Optional[Path]:
+            try:
+                skills_dir.mkdir(parents=True, exist_ok=True)
+                if not skills_dir.is_dir():
+                    raise NotADirectoryError(f"{skills_dir} is not a directory")
+            except (OSError, ValueError) as exc:
+                _print_cli_warning(
+                    "resolve", "skills directory", str(skills_dir), exc,
+                    continuing="Continuing without skill registration.",
+                )
+                return None
+            return skills_dir
+
         try:
-            return resolve_active_skills_dir(self.project_root)
+            skills_dir = resolve_active_skills_dir(self.project_root)
         except (ValueError, OSError) as exc:
             _print_cli_warning(
                 "resolve", "skills directory", None, exc,
                 continuing="Continuing without skill registration.",
             )
             return None
+        if skills_dir is None:
+            return None
+
+        opts = load_init_options(self.project_root)
+        if not isinstance(opts, dict):
+            return _ensure_usable(skills_dir)
+        selected_ai = opts.get("ai")
+        if not isinstance(selected_ai, str) or not selected_ai:
+            return _ensure_usable(skills_dir)
+
+        from .agents import CommandRegistrar
+
+        registrar = CommandRegistrar()
+        agent_config = registrar.AGENT_CONFIGS.get(selected_ai)
+        if agent_config and agent_config.get("extension") == "/SKILL.md":
+            agent_skills_dir = registrar._resolve_agent_dir(
+                selected_ai, agent_config, self.project_root
+            )
+            return _ensure_usable(agent_skills_dir)
+        return _ensure_usable(skills_dir)
 
     def _register_extension_skills(
         self,
@@ -1249,7 +1288,11 @@ class ExtensionManager:
             registrar = CommandRegistrar()
             # Register for all detected agents
             registered_commands = registrar.register_commands_for_all_agents(
-                manifest, dest_dir, self.project_root, link_outputs=link_commands
+                manifest,
+                dest_dir,
+                self.project_root,
+                link_outputs=link_commands,
+                create_missing_active_skills_dir=True,
             )
 
         # Auto-register extension commands as agent skills when --ai-skills
@@ -1540,9 +1583,10 @@ class ExtensionManager:
             init_options = {}
 
         active_agent = init_options.get("ai")
+        ai_skills_enabled = is_ai_skills_enabled(init_options)
         skills_mode_active = (
             active_agent == agent_name
-            and bool(init_options.get("ai_skills"))
+            and ai_skills_enabled
             and bool(agent_config)
             and agent_config.get("extension") != "/SKILL.md"
         )
@@ -1736,6 +1780,7 @@ class CommandRegistrar:
         extension_dir: Path,
         project_root: Path,
         link_outputs: bool = False,
+        create_missing_active_skills_dir: bool = False,
     ) -> Dict[str, List[str]]:
         """Register extension commands for all detected agents."""
         context_note = f"\n<!-- Extension: {manifest.id} -->\n<!-- Config: .specify/extensions/{manifest.id}/ -->\n"
@@ -1743,6 +1788,7 @@ class CommandRegistrar:
             manifest.commands, manifest.id, extension_dir, project_root,
             context_note=context_note,
             link_outputs=link_outputs,
+            create_missing_active_skills_dir=create_missing_active_skills_dir,
         )
 
     def unregister_commands(
@@ -2530,10 +2576,11 @@ class HookExecutor:
 
         init_options = self._load_init_options()
         selected_ai = init_options.get("ai")
-        codex_skill_mode = selected_ai == "codex" and bool(init_options.get("ai_skills"))
-        claude_skill_mode = selected_ai == "claude" and bool(init_options.get("ai_skills"))
+        ai_skills_enabled = is_ai_skills_enabled(init_options)
+        codex_skill_mode = selected_ai == "codex" and ai_skills_enabled
+        claude_skill_mode = selected_ai == "claude" and ai_skills_enabled
         kimi_skill_mode = selected_ai == "kimi"
-        cursor_skill_mode = selected_ai == "cursor-agent" and bool(init_options.get("ai_skills"))
+        cursor_skill_mode = selected_ai == "cursor-agent" and ai_skills_enabled
         cline_mode = selected_ai == "cline"
 
         skill_name = self._skill_name_from_command(command_id)