fix pr comment

Author: davidebibm

src/specify_cli/integrations/_helpers.py

@@ -279,14 +279,18 @@ def _update_init_options_for_integration(
     opts["speckit_version"] = _get_speckit_version()
     if script_type:
         opts["script"] = script_type
-    # Skills mode is either intrinsic (SkillsIntegration), set on the instance
-    # during setup() (_skills_mode), or requested via parsed options (e.g.
-    # Copilot's --skills, persisted as parsed_options["skills"]). The latter is
-    # the only signal available on the `use` path, where no setup() runs and a
-    # fresh integration instance has _skills_mode == False (issue #3550).
+    # Skills mode is either intrinsic (SkillsIntegration), derived from
+    # parsed_options via a callable _skills_mode method (e.g. Bob), set on
+    # the instance during setup() as a bool attribute (e.g. Copilot), or
+    # requested via parsed options (e.g. Copilot's --skills, persisted as
+    # parsed_options["skills"]). The latter is the only signal available on
+    # the `use` path, where no setup() runs and a fresh integration instance
+    # has _skills_mode == False (issue #3550).
+    _skills_mode_attr = getattr(integration, "_skills_mode", None)
     skills_mode = (
         isinstance(integration, SkillsIntegration)
-        or getattr(integration, "_skills_mode", False)
+        or (callable(_skills_mode_attr) and _skills_mode_attr(parsed_options))
+        or (not callable(_skills_mode_attr) and bool(_skills_mode_attr))
         or bool((parsed_options or {}).get("skills"))
     )
     if skills_mode:

tests/integrations/test_integration_bob.py

@@ -300,6 +300,30 @@ def test_init_legacy_creates_commands(self, tmp_path):
         assert (target / ".bob" / "commands" / "speckit.plan.md").exists()
         assert not (target / ".bob" / "skills").exists()
 
+    def test_init_legacy_does_not_set_ai_skills(self, tmp_path):
+        """Legacy install must NOT write ai_skills=True to init-options.json.
+
+        Regression test: _update_init_options_for_integration previously called
+        getattr(integration, "_skills_mode", False) which returned the bound method
+        object (always truthy) instead of calling it, so legacy projects incorrectly
+        got ai_skills=True and used hyphenated skill invocations.
+        """
+        from typer.testing import CliRunner
+        from specify_cli import app
+        from specify_cli import load_init_options
+
+        target = tmp_path / "test-proj"
+        result = CliRunner().invoke(app, [
+            "init", str(target), "--integration", "bob",
+            "--integration-options", "--legacy-commands",
+            "--ignore-agent-tools", "--script", "sh",
+        ])
+        assert result.exit_code == 0, f"init failed: {result.output}"
+        init_opts = load_init_options(target)
+        assert init_opts.get("ai_skills") is not True, (
+            "Legacy Bob project must not have ai_skills=True in init-options.json"
+        )
+
 
 class TestBobRegistrarConfig:
     """Verify AGENT_CONFIGS["bob"] follows the Copilot pattern for extension registration."""