refactor: create commands/ package and move init handler (PR-4/8) (#2615)

* refactor: create commands/ package and move init handler (PR-4/8)

- Extract agent configuration constants (AGENT_CONFIG, AI_ASSISTANT_HELP,
  SCRIPT_TYPE_CHOICES, etc.) to _agent_config.py to avoid circular imports
- Create commands/ package skeleton with stub modules for each command group
- Move init command handler (~670 lines) from __init__.py to commands/init.py
  using the register(app) pattern; lazy imports inside the handler body
  prevent circular dependencies with __init__.py
- Re-export AGENT_CONFIG, AI_ASSISTANT_HELP, SCRIPT_TYPE_CHOICES from
  __init__.py for backward compatibility
- Add tests/test_commands_package.py to verify package structure

* fix(tests): update patch targets after moving init handler to commands/init.py

_stdin_is_interactive and select_with_arrows are now bound in
specify_cli.commands.init, not specify_cli directly.

* fix(lint): remove unused imports and mark re-exports in __init__.py

- Remove shutil, shlex top-level imports (used lazily inside functions)
- Remove rich.live.Live import (moved to commands/init.py)
- Mark select_with_arrows and _locate_bundled_workflow as explicit
  re-exports to satisfy ruff F401

* chore: add from __future__ import annotations to new modules

Aligns with the project convention established in _console.py, _assets.py,
_utils.py, and other modules.

* docs(cli): align init help with bundled scaffolding

Potential fix for pull request finding

Update command package documentation and init help text to reflect the current implementation: init uses bundled assets and integration setup, while placeholder command modules are import anchors until extracted. Remove the unused tracker-active flag assignment that had no reader in the codebase.

Constraint: --offline is hidden/no-op and init no longer downloads templates from GitHub releases

Rejected: Add no-op register functions to placeholder modules | would imply extracted command groups are implemented there

Confidence: high

Scope-risk: narrow

Directive: Keep CLI help text aligned with the actual init scaffolding path

Tested: uv run specify init --help; uv run pytest tests/test_commands_package.py tests/test_agent_config_consistency.py -q; uv run pytest tests/test_commands_package.py tests/test_console_imports.py tests/integrations/test_cli.py -q

Not-tested: full test suite

* fix(init): align preset failure reporting with _print_cli_warning helper

Use the _print_cli_warning helper (introduced in main) for preset install
failures so that output matches the expected format:
  "Failed to install preset '<name>': ..."
  "Continuing without the optional preset."

* fix(init): remove unused lazy imports

The init command imported CLI error formatting helpers through its circular-dependency-safe lazy import block, but the module does not use them. Remove those imports so ruff does not report F401.

Constraint: uvx ruff check src/ must pass.

Rejected: Wire the helpers into init error handling | Existing preset warnings already use _print_cli_warning, and changing behavior is unnecessary for this lint fix.

Confidence: high

Scope-risk: narrow

Directive: Keep lazy import blocks limited to names consumed in the importing module.

Tested: uvx ruff check src/

Not-tested: Full pytest suite

Co-authored-by: OmX <omx@oh-my-codex.dev>

---------

Co-authored-by: OmX <omx@oh-my-codex.dev>

tests/test_commands_package.py

@@ -0,0 +1,48 @@
+"""Tests for the commands/ package structure."""
+import importlib
+
+
+def test_commands_package_importable():
+    mod = importlib.import_module("specify_cli.commands")
+    assert mod is not None
+
+
+def test_commands_init_importable():
+    mod = importlib.import_module("specify_cli.commands.init")
+    assert hasattr(mod, "register")
+    assert callable(mod.register)
+
+
+def test_commands_stubs_importable():
+    for name in ("integration", "preset", "extension", "workflow"):
+        mod = importlib.import_module(f"specify_cli.commands.{name}")
+        assert mod is not None
+
+
+def test_agent_config_importable():
+    from specify_cli._agent_config import (
+        AGENT_CONFIG,
+        AI_ASSISTANT_ALIASES,
+        AI_ASSISTANT_HELP,
+        DEFAULT_INIT_INTEGRATION,
+        SCRIPT_TYPE_CHOICES,
+    )
+    assert isinstance(AGENT_CONFIG, dict)
+    assert isinstance(AI_ASSISTANT_ALIASES, dict)
+    assert isinstance(AI_ASSISTANT_HELP, str)
+    assert DEFAULT_INIT_INTEGRATION == "copilot"
+    assert "sh" in SCRIPT_TYPE_CHOICES
+
+
+def test_agent_config_re_exported_from_init():
+    from specify_cli import AGENT_CONFIG, AI_ASSISTANT_ALIASES, AI_ASSISTANT_HELP, SCRIPT_TYPE_CHOICES
+    assert isinstance(AGENT_CONFIG, dict)
+    assert "sh" in SCRIPT_TYPE_CHOICES
+
+
+def test_init_command_registered():
+    from specify_cli import app
+    callback_names = [
+        cmd.callback.__name__ for cmd in app.registered_commands if cmd.callback
+    ]
+    assert "init" in callback_names