refactor(integrations): co-locate integration commands in integrations/ domain dir (PR-5/8) (#2720)

* 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

* fix(integrations): restore original integration list output in refactor

Preserve the CLI Required column, post-table default/installed summary,
and no-installed guidance that were dropped during the no-behavior-change
refactor of integration list into _query_commands.py.

* Potential fix for pull request finding

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>

* fix(integrations): restore _clear/_update_init_options public imports

The refactor that split integration commands moved
_clear_init_options_for_integration and _update_init_options_for_integration
into integrations/_helpers.py, but tests still import them from the top-level
specify_cli package, causing ImportError. Re-export them with explicit aliases
at the end of __init__.py to preserve the public import surface.

---------

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>

src/specify_cli/integrations/_commands.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")