refactor(integrations): co-locate integration commands in integrations/ domain dir

- Remove commands/ stubs (handlers will live in domain dirs)
- Move all integration CLI handlers out of __init__.py into integrations/
- Split into focused modules under integrations/:
    _helpers.py           (340 lines) — domain helpers
    _install_commands.py  (306 lines) — install / uninstall
    _migrate_commands.py  (487 lines) — switch / upgrade
    _query_commands.py    (442 lines) — list / use / search / info / catalog
    _commands.py           (34 lines) — app objects + register()
- __init__.py reduced by ~1400 lines; integration block replaced with register() call
- Fix patch paths in tests to new module locations

Author: darion-yaphet

src/specify_cli/__init__.py

@@ -151,12 +151,14 @@ def init(
         # Lazy imports to avoid circular dependency — __init__.py imports this module
         from .. import (
             _install_shared_infra_or_exit,
-            _parse_integration_options,
             _print_cli_warning,
-            _write_integration_json,
             ensure_executable_scripts,
             save_init_options,
         )
+        from ..integrations._commands import (
+            _parse_integration_options,
+            _write_integration_json,
+        )
         from ..integration_runtime import with_integration_setting as _with_integration_setting
 
         show_banner()

src/specify_cli/commands/extension.py

@@ -0,0 +1,34 @@
+"""specify integration * commands — app objects and register() entry point."""
+from __future__ import annotations
+
+import typer
+
+from .._assets import get_speckit_version  # noqa: F401 — re-exported for monkeypatching in tests
+
+# Re-export helpers used by commands/init.py and tests
+from ._helpers import (  # noqa: F401
+    _cli_error_detail,
+    _cli_phase_label,
+    _parse_integration_options,
+    _write_integration_json,
+)
+
+integration_app = typer.Typer(
+    name="integration",
+    help="Manage coding agent integrations",
+    add_completion=False,
+)
+
+integration_catalog_app = typer.Typer(
+    name="catalog",
+    help="Manage integration catalog sources",
+    add_completion=False,
+)
+integration_app.add_typer(integration_catalog_app, name="catalog")
+
+
+def register(app: typer.Typer) -> None:
+    from . import _install_commands  # noqa: F401 — registers handlers via decorators
+    from . import _migrate_commands  # noqa: F401
+    from . import _query_commands    # noqa: F401
+    app.add_typer(integration_app, name="integration")