address 3 comments from copilot

Author: davidebibm

src/specify_cli/commands/init.py

@@ -501,10 +501,13 @@ def init(
                 _legacy_commands = bool(
                     (integration_parsed_options or {}).get("legacy_commands")
                 )
-                if (
+                _skills_mode_attr = getattr(resolved_integration, "_skills_mode", None)
+                _is_skills = (
                     isinstance(resolved_integration, _SkillsPersist)
-                    or getattr(resolved_integration, "_skills_mode", False)
-                ) and not _legacy_commands:
+                    or (callable(_skills_mode_attr) and _skills_mode_attr(integration_parsed_options))
+                    or (not callable(_skills_mode_attr) and bool(_skills_mode_attr))
+                )
+                if _is_skills and not _legacy_commands:
                     init_opts["ai_skills"] = True
                 save_init_options(project_path, init_opts)
 
@@ -648,9 +651,12 @@ def init(
 
         from ..integrations.base import SkillsIntegration as _SkillsInt
 
-        _is_skills_integration = isinstance(
-            resolved_integration, _SkillsInt
-        ) or getattr(resolved_integration, "_skills_mode", False)
+        _skills_mode_attr = getattr(resolved_integration, "_skills_mode", None)
+        _is_skills_integration = (
+            isinstance(resolved_integration, _SkillsInt)
+            or (callable(_skills_mode_attr) and _skills_mode_attr(integration_parsed_options))
+            or (not callable(_skills_mode_attr) and bool(_skills_mode_attr))
+        )
 
         codex_skill_mode = selected_ai == "codex" and _is_skills_integration
         zcode_skill_mode = selected_ai == "zcode" and _is_skills_integration

src/specify_cli/integrations/_helpers.py

@@ -252,6 +252,7 @@ def _update_init_options_for_integration(
     project_root: Path,
     integration: Any,
     script_type: str | None = None,
+    parsed_options: dict[str, Any] | None = None,
 ) -> None:
     """Update init-options.json to reflect *integration* as the active one.
 
@@ -270,7 +271,12 @@ def _update_init_options_for_integration(
     opts["speckit_version"] = _get_speckit_version()
     if script_type:
         opts["script"] = script_type
-    if isinstance(integration, SkillsIntegration) or getattr(integration, "_skills_mode", False):
+    _skills_mode_attr = getattr(integration, "_skills_mode", None)
+    if callable(_skills_mode_attr):
+        is_skills = _skills_mode_attr(parsed_options)
+    else:
+        is_skills = bool(_skills_mode_attr) or isinstance(integration, SkillsIntegration)
+    if is_skills:
         opts["ai_skills"] = True
     else:
         opts.pop("ai_skills", None)
@@ -326,7 +332,9 @@ def _set_default_integration(
             ) from exc
 
     _write_integration_json(project_root, key, installed_keys, settings)
-    _update_init_options_for_integration(project_root, integration, script_type=resolved_script)
+    _update_init_options_for_integration(
+        project_root, integration, script_type=resolved_script, parsed_options=parsed_options
+    )
 
 
 def _set_default_integration_or_exit(*args: Any, **kwargs: Any) -> None:

src/specify_cli/integrations/_install_commands.py

@@ -158,7 +158,9 @@ def integration_install(
         )
         _write_integration_json(project_root, new_default, new_installed, settings)
         if new_default == integration.key:
-            _update_init_options_for_integration(project_root, integration, script_type=selected_script)
+            _update_init_options_for_integration(
+                project_root, integration, script_type=selected_script, parsed_options=parsed_options
+            )
         else:
             _refresh_init_options_speckit_version(project_root)
 

src/specify_cli/integrations/_migrate_commands.py

@@ -463,7 +463,9 @@ def integration_upgrade(
         new_manifest.save()
         _write_integration_json(project_root, installed_key, installed_keys, settings)
         if installed_key == key:
-            _update_init_options_for_integration(project_root, integration, script_type=selected_script)
+            _update_init_options_for_integration(
+                project_root, integration, script_type=selected_script, parsed_options=parsed_options
+            )
         else:
             _refresh_init_options_speckit_version(project_root)
     except Exception as exc:

src/specify_cli/integrations/bob/__init__.py

@@ -77,6 +77,10 @@ class _BobSkillsHelper(SkillsIntegration):
         "extension": "/SKILL.md",
     }
 
+    def post_process_skill_content(self, content: str) -> str:
+        """Bob skills are intent-activated; no slash-command note is needed."""
+        return content
+
 
 class BobIntegration(IntegrationBase):
     """Integration for IBM Bob IDE.
@@ -121,17 +125,16 @@ def effective_invoke_separator(
         "extension": "/SKILL.md",
     }
 
-    @property
-    def _skills_mode(self) -> bool:
+    def _skills_mode(self, parsed_options: dict[str, Any] | None = None) -> bool:
         """True when the instance is configured in skills (default) mode.
 
-        Derived from the current ``registrar_config`` so that the value
-        reflects whichever mode ``setup()`` last activated, without relying
-        on mutable instance state that is unavailable in a fresh process
-        (e.g. ``specify integration use bob`` or ``_set_default_integration``).
+        Derived from *parsed_options* so that the value is correct both
+        during ``setup()`` and in fresh-process contexts where ``setup()``
+        has not been called (e.g. ``specify integration use bob``).
         """
-        rc = self.registrar_config or {}
-        return rc.get("extension") == "/SKILL.md"
+        if parsed_options is None:
+            parsed_options = {}
+        return not parsed_options.get("legacy_commands", False)
 
     @classmethod
     def options(cls) -> list[IntegrationOption]:
@@ -163,13 +166,9 @@ def setup(
         """
         parsed_options = parsed_options or {}
         if parsed_options.get("legacy_commands"):
-            self.registrar_config = dict(_BobMarkdownHelper.registrar_config)
             _warn_legacy_commands_deprecated()
             return self._setup_legacy(project_root, manifest, parsed_options, **opts)
-        self.registrar_config = dict(_BobSkillsHelper.registrar_config)
-        return SkillsIntegration.setup(
-            _BobSkillsHelper(), project_root, manifest, parsed_options, **opts
-        )
+        return _BobSkillsHelper().setup(project_root, manifest, parsed_options, **opts)
 
     def _setup_legacy(
         self,