fix: address PR review round 3

- Clarify parsed_options forwarding is intentional (all options passed,
  integrations decide what to use)
- Extract _strip_ansi() helper in test_extensions.py and test_presets.py
- Remove unused pytest import (test_cli.py), unused locals (test_integration_base_skills.py)
- Reword --ai-commands-dir deprecation to be actionable without referencing
  the not-yet-implemented --integration-options

Author: mnriem

src/specify_cli/__init__.py

@@ -2248,7 +2248,9 @@ def init(
                     resolved_integration.key, project_path, version=get_speckit_version()
                 )
 
-                # Build parsed_options from legacy CLI flags for Stage 5 integrations
+                # Forward all legacy CLI flags to the integration as parsed_options.
+                # Integrations receive every option and decide what to use;
+                # irrelevant keys are simply ignored by the integration's setup().
                 integration_parsed_options: dict[str, Any] = {}
                 if ai_commands_dir:
                     integration_parsed_options["commands_dir"] = ai_commands_dir

tests/integrations/test_cli.py

@@ -3,8 +3,6 @@
 import json
 import os
 
-import pytest
-
 
 class TestInitIntegrationFlag:
     def test_integration_and_ai_mutually_exclusive(self, tmp_path):

tests/integrations/test_integration_base_skills.py

@@ -97,7 +97,6 @@ def test_skill_directory_structure(self, tmp_path):
         i = get_integration(self.KEY)
         m = IntegrationManifest(self.KEY, tmp_path)
         created = i.setup(tmp_path, m)
-        skills_dir = i.skills_dest(tmp_path)
         skill_files = [f for f in created if "scripts" not in f.parts]
 
         expected_commands = {
@@ -223,7 +222,7 @@ def test_pre_existing_skills_not_removed(self, tmp_path):
     def test_setup_installs_update_context_scripts(self, tmp_path):
         i = get_integration(self.KEY)
         m = IntegrationManifest(self.KEY, tmp_path)
-        created = i.setup(tmp_path, m)
+        i.setup(tmp_path, m)
         scripts_dir = tmp_path / ".specify" / "integrations" / self.KEY / "scripts"
         assert scripts_dir.is_dir(), f"Scripts directory not created for {self.KEY}"
         assert (scripts_dir / "update-context.sh").exists()

tests/test_extensions.py

@@ -9,6 +9,7 @@
 - Catalog stack (multi-catalog support)
 """
 
+import re
 import pytest
 import json
 import tempfile
@@ -33,6 +34,11 @@
 )
 
 
+def _strip_ansi(text: str) -> str:
+    """Remove ANSI escape codes from Rich-formatted CLI output."""
+    return re.sub(r'\x1b\[[0-9;]*m', '', text)
+
+
 # ===== Fixtures =====
 
 @pytest.fixture
@@ -3126,8 +3132,7 @@ def test_list_shows_extension_id(self, extension_dir, project_dir):
             result = runner.invoke(app, ["extension", "list"])
 
         assert result.exit_code == 0, result.output
-        import re as _re
-        plain = _re.sub(r'\x1b\[[0-9;]*m', '', result.output)
+        plain = _strip_ansi(result.output)
         # Verify the extension ID is shown in the output
         assert "test-ext" in plain
         # Verify name and version are also shown
@@ -3362,8 +3367,7 @@ def test_list_shows_priority(self, extension_dir, project_dir):
             result = runner.invoke(app, ["extension", "list"])
 
         assert result.exit_code == 0, result.output
-        import re as _re
-        plain = _re.sub(r'\x1b\[[0-9;]*m', '', result.output)
+        plain = _strip_ansi(result.output)
         assert "Priority: 7" in plain
 
     def test_set_priority_changes_priority(self, extension_dir, project_dir):
@@ -3385,8 +3389,7 @@ def test_set_priority_changes_priority(self, extension_dir, project_dir):
             result = runner.invoke(app, ["extension", "set-priority", "test-ext", "5"])
 
         assert result.exit_code == 0, result.output
-        import re as _re
-        plain = _re.sub(r'\x1b\[[0-9;]*m', '', result.output)
+        plain = _strip_ansi(result.output)
         assert "priority changed: 10 → 5" in plain
 
         # Reload registry to see updated value
@@ -3409,8 +3412,7 @@ def test_set_priority_same_value_no_change(self, extension_dir, project_dir):
             result = runner.invoke(app, ["extension", "set-priority", "test-ext", "5"])
 
         assert result.exit_code == 0, result.output
-        import re as _re
-        plain = _re.sub(r'\x1b\[[0-9;]*m', '', result.output)
+        plain = _strip_ansi(result.output)
         assert "already has priority 5" in plain
 
     def test_set_priority_invalid_value(self, extension_dir, project_dir):

tests/test_presets.py

@@ -11,6 +11,7 @@
 """
 
 import pytest
+import re
 import json
 import tempfile
 import shutil
@@ -35,6 +36,11 @@
 from specify_cli.extensions import ExtensionRegistry
 
 
+def _strip_ansi(text: str) -> str:
+    """Remove ANSI escape codes from Rich-formatted CLI output."""
+    return re.sub(r'\x1b\[[0-9;]*m', '', text)
+
+
 # ===== Fixtures =====
 
 
@@ -2441,8 +2447,7 @@ def test_set_priority_changes_priority(self, project_dir, pack_dir):
             result = runner.invoke(app, ["preset", "set-priority", "test-pack", "5"])
 
         assert result.exit_code == 0, result.output
-        import re as _re
-        plain = _re.sub(r'\x1b\[[0-9;]*m', '', result.output)
+        plain = _strip_ansi(result.output)
         assert "priority changed: 10 → 5" in plain
 
         # Reload registry to see updated value
@@ -2465,8 +2470,7 @@ def test_set_priority_same_value_no_change(self, project_dir, pack_dir):
             result = runner.invoke(app, ["preset", "set-priority", "test-pack", "5"])
 
         assert result.exit_code == 0, result.output
-        import re as _re
-        plain = _re.sub(r'\x1b\[[0-9;]*m', '', result.output)
+        plain = _strip_ansi(result.output)
         assert "already has priority 5" in plain
 
     def test_set_priority_invalid_value(self, project_dir, pack_dir):