refactor: move extension command handlers to extensions/_commands.py (PR-7/8)

[darion-yaphet]

Summary

PR-7 of the 8-part effort to break up the specify_cli/__init__.py monolith. Continues the domain-dir layout established in PR-5 (integrations/_commands.py) and PR-6 (presets/_commands.py).

This PR moves the extension * and catalog * command handlers out of __init__.py. Because extensions was a flat module (unlike the already-package presets/integrations), it is first converted to a package.

Changes

• extensions.py → extensions/__init__.py — pure rename (99% identical). The module's intra-file relative imports are bumped from .x to ..x, since they reference root-package siblings (.._init_options, ..catalogs, ..agents, ..integrations, and from .. import for load_init_options, _print_cli_warning, AGENT_CONFIG, DEFAULT_SKILLS_DIR, _get_skills_dir).
• New extensions/_commands.py — holds extension_app, catalog_app, all 12 command handlers (list/add/remove/search/info/update/enable/disable/set-priority + catalog list/add/remove), the private helpers (_resolve_installed_extension, _resolve_catalog_extension, _print_extension_info), and a register(app) entry point.
• __init__.py drops ~1444 lines (3511 → 2067). The extension command group is re-attached via register(app), preserving the CLI surface.

Monkeypatch compatibility

Root helpers (_require_specify_project, _locate_bundled_extension, load_init_options, _display_project_path) are reached through thin shims in _commands.py that re-fetch from the parent package at call time. This keeps existing specify_cli.<helper> monkeypatch targets working with no test changes.

Verification

• extension/catalog command tree loads and all --help surfaces respond.
• Full test suite failure set is identical before and after this change (82 pre-existing environment failures unrelated to the refactor; 0 new, 0 fixed-by-accident).

No behavior change — pure structural move.

[Copilot]

Pull request overview

Refactors the Specify CLI by extracting specify extension * and specify extension catalog * command handlers out of the specify_cli/__init__.py monolith into a dedicated extensions/_commands.py module, while converting extensions from a flat module into a package to support the domain-dir layout.

Changes:

• Introduces src/specify_cli/extensions/_commands.py containing the Typer apps (extension, catalog) and all related command handlers, plus a register(app) entry point.
• Converts extensions.py into extensions/__init__.py and updates intra-package imports accordingly.
• Re-attaches the extension command group from specify_cli/__init__.py via _register_extension_cmds(app) to preserve the CLI surface.

Show a summary per file

File	Description
src/specify_cli/extensions/_commands.py	New home for extension / catalog Typer apps and all extension-related CLI handlers (registered via register(app)).
src/specify_cli/extensions/init.py	Converts extensions into a package and adjusts relative imports to continue referencing root-package siblings.
src/specify_cli/init.py	Removes inline extension command definitions and registers the new extensions command module to keep the same CLI entry points.

Copilot's findings

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• Files reviewed: 3/3 changed files
• Comments generated: 3

[mnriem]

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