feat!: remove legacy --ai, --ai-commands-dir, and --ai-skills flags (0.10.0) (#2872)

* Initial plan

* feat!: remove legacy --ai, --ai-commands-dir, and --ai-skills flags at 0.10.0

* refactor(tests): rename stale test_ai_help_* methods to test_agent_config_*

* fix: address review — derive agent folder for generic integration and remove redundant test

- Security notice now falls back to integration_parsed_options['commands_dir']
  when AGENT_CONFIG folder is None (generic integration).
- Remove test_agent_config_includes_kiro_cli which duplicates the assertion
  in test_runtime_config_uses_kiro_cli_and_removes_q.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* docs: scrub all remaining --ai flag references from source and tests

- Remove dead AI_ASSISTANT_ALIASES, AI_ASSISTANT_HELP, and
  _build_ai_assistant_help() from _agent_config.py
- Update comments/docstrings in extensions.py, presets.py, and
  integration subpackages to reference 'skills mode' or
  '--integration' instead of the removed flags
- Fix catalog.json generic integration description
- Update test docstrings/comments in test_extension_skills.py,
  test_extensions.py, and test_presets.py

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* test: remove legacy --ai flag rejection tests

The flags are fully removed from the CLI; typer handles unknown options
generically. No custom rejection logic exists to test.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* revert: remove manual CHANGELOG.md entry

CHANGELOG is generated automatically; manual edits should not be made.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix: make generic catalog description self-explanatory

Include the required --commands-dir sub-option in the description so
readers don't need to look up integration docs.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* fix(tests): rename duplicate test classes to avoid shadowing

The rename from Test*AutoPromote to Test*Integration collided with the
existing Test*Integration(SkillsIntegrationTests) base classes, causing
the shared test suites to be silently overwritten. Rename the CLI init
flow classes to Test*InitFlow instead.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: Manfred Riem <mnriem@users.noreply.github.com>
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

tests/integrations/test_integration_codex.py

@@ -14,19 +14,19 @@ class TestCodexIntegration(SkillsIntegrationTests):
     CONTEXT_FILE = "AGENTS.md"
 
 
-class TestCodexAutoPromote:
-    """--ai codex auto-promotes to integration path."""
+class TestCodexInitFlow:
+    """--integration codex creates expected files."""
 
-    def test_ai_codex_without_ai_skills_auto_promotes(self, tmp_path):
-        """--ai codex should work the same as --integration codex."""
+    def test_integration_codex_creates_skills(self, tmp_path):
+        """--integration codex should create skills in .agents/skills."""
         from typer.testing import CliRunner
         from specify_cli import app
 
         runner = CliRunner()
         target = tmp_path / "test-proj"
-        result = runner.invoke(app, ["init", str(target), "--ai", "codex", "--no-git", "--ignore-agent-tools", "--script", "sh"])
+        result = runner.invoke(app, ["init", str(target), "--integration", "codex", "--no-git", "--ignore-agent-tools", "--script", "sh"])
 
-        assert result.exit_code == 0, f"init --ai codex failed: {result.output}"
+        assert result.exit_code == 0, f"init --integration codex failed: {result.output}"
         assert (target / ".agents" / "skills" / "speckit-plan" / "SKILL.md").exists()