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_cli.py

@@ -43,16 +43,6 @@ class TestCliDiagnosticFormatting:
 
 
 class TestInitIntegrationFlag:
-    def test_integration_and_ai_mutually_exclusive(self, tmp_path):
-        from typer.testing import CliRunner
-        from specify_cli import app
-        runner = CliRunner()
-        result = runner.invoke(app, [
-            "init", str(tmp_path / "test-project"), "--ai", "claude", "--integration", "copilot",
-        ])
-        assert result.exit_code != 0
-        assert "mutually exclusive" in result.output
-
     def test_unknown_integration_rejected(self, tmp_path):
         from typer.testing import CliRunner
         from specify_cli import app
@@ -131,7 +121,7 @@ class TestInitIntegrationFlag:
         data = json.loads((project / ".specify" / "integration.json").read_text(encoding="utf-8"))
         assert data["integration"] == specify_cli.DEFAULT_INIT_INTEGRATION
 
-    def test_ai_copilot_auto_promotes(self, tmp_path):
+    def test_integration_copilot_auto_promotes(self, tmp_path):
         from typer.testing import CliRunner
         from specify_cli import app
         project = tmp_path / "promote-test"
@@ -141,66 +131,13 @@ class TestInitIntegrationFlag:
             os.chdir(project)
             runner = CliRunner()
             result = runner.invoke(app, [
-                "init", "--here", "--ai", "copilot", "--script", "sh", "--no-git",
+                "init", "--here", "--integration", "copilot", "--script", "sh", "--no-git",
             ], catch_exceptions=False)
         finally:
             os.chdir(old_cwd)
         assert result.exit_code == 0
         assert (project / ".github" / "agents" / "speckit.plan.agent.md").exists()
 
-    def test_ai_emits_deprecation_warning_with_integration_replacement(self, tmp_path):
-        from typer.testing import CliRunner
-        from specify_cli import app
-
-        project = tmp_path / "warn-ai"
-        project.mkdir()
-        old_cwd = os.getcwd()
-        try:
-            os.chdir(project)
-            runner = CliRunner()
-            result = runner.invoke(app, [
-                "init", "--here", "--ai", "copilot", "--script", "sh", "--no-git",
-            ], catch_exceptions=False)
-        finally:
-            os.chdir(old_cwd)
-
-        normalized_output = _normalize_cli_output(result.output)
-        assert result.exit_code == 0, result.output
-        assert "Deprecation Warning" in normalized_output
-        assert "--ai" in normalized_output
-        assert "deprecated" in normalized_output
-        assert "no longer be available" in normalized_output
-        assert "0.10.0" in normalized_output
-        assert "--integration copilot" in normalized_output
-        assert normalized_output.index("Deprecation Warning") < normalized_output.index("Next Steps")
-        assert (project / ".github" / "agents" / "speckit.plan.agent.md").exists()
-
-    def test_ai_generic_warning_suggests_integration_options_equivalent(self, tmp_path):
-        from typer.testing import CliRunner
-        from specify_cli import app
-
-        project = tmp_path / "warn-generic"
-        project.mkdir()
-        old_cwd = os.getcwd()
-        try:
-            os.chdir(project)
-            runner = CliRunner()
-            result = runner.invoke(app, [
-                "init", "--here", "--ai", "generic", "--ai-commands-dir", ".myagent/commands",
-                "--script", "sh", "--no-git",
-            ], catch_exceptions=False)
-        finally:
-            os.chdir(old_cwd)
-
-        normalized_output = _normalize_cli_output(result.output)
-        assert result.exit_code == 0, result.output
-        assert "Deprecation Warning" in normalized_output
-        assert "--integration generic" in normalized_output
-        assert "--integration-options" in normalized_output
-        assert ".myagent/commands" in normalized_output
-        assert normalized_output.index("Deprecation Warning") < normalized_output.index("Next Steps")
-        assert (project / ".myagent" / "commands" / "speckit.plan.md").exists()
-
     def test_init_optional_preset_failure_reports_target_and_continues(
         self, tmp_path, monkeypatch
     ):
@@ -237,7 +174,7 @@ class TestInitIntegrationFlag:
         assert "Continuing without the optional preset" in normalized
         assert "Project ready" in normalized
 
-    def test_ai_claude_here_preserves_preexisting_commands(self, tmp_path):
+    def test_integration_claude_here_preserves_preexisting_commands(self, tmp_path):
         from typer.testing import CliRunner
         from specify_cli import app
 
@@ -255,7 +192,7 @@ class TestInitIntegrationFlag:
             os.chdir(project)
             runner = CliRunner()
             result = runner.invoke(app, [
-                "init", "--here", "--force", "--ai", "claude", "--ai-skills", "--script", "sh", "--no-git", "--ignore-agent-tools",
+                "init", "--here", "--force", "--integration", "claude", "--script", "sh", "--no-git", "--ignore-agent-tools",
             ], catch_exceptions=False)
         finally:
             os.chdir(old_cwd)
@@ -800,7 +737,7 @@ class TestGitExtensionAutoInstall:
             os.chdir(project)
             runner = CliRunner()
             result = runner.invoke(app, [
-                "init", "--here", "--ai", "claude", "--script", "sh",
+                "init", "--here", "--integration", "claude", "--script", "sh",
                 "--ignore-agent-tools",
             ], catch_exceptions=False)
         finally:
@@ -838,7 +775,7 @@ class TestGitExtensionAutoInstall:
             os.chdir(project)
             runner = CliRunner()
             result = runner.invoke(app, [
-                "init", "--here", "--ai", "claude", "--script", "sh",
+                "init", "--here", "--integration", "claude", "--script", "sh",
                 "--no-git", "--ignore-agent-tools",
             ], catch_exceptions=False)
         finally:
@@ -862,7 +799,7 @@ class TestGitExtensionAutoInstall:
             os.chdir(project)
             runner = CliRunner()
             result = runner.invoke(app, [
-                "init", "--here", "--ai", "claude", "--script", "sh",
+                "init", "--here", "--integration", "claude", "--script", "sh",
                 "--no-git", "--ignore-agent-tools",
             ], catch_exceptions=False)
         finally:
@@ -889,7 +826,7 @@ class TestGitExtensionAutoInstall:
             os.chdir(project)
             runner = CliRunner()
             result = runner.invoke(app, [
-                "init", "--here", "--ai", "claude", "--script", "sh",
+                "init", "--here", "--integration", "claude", "--script", "sh",
                 "--ignore-agent-tools",
             ], catch_exceptions=False)
         finally:
@@ -915,7 +852,7 @@ class TestGitExtensionAutoInstall:
             os.chdir(project)
             runner = CliRunner()
             result = runner.invoke(app, [
-                "init", "--here", "--ai", "claude", "--script", "sh",
+                "init", "--here", "--integration", "claude", "--script", "sh",
                 "--ignore-agent-tools",
             ], catch_exceptions=False)
         finally: