refactor: reorganize bundle CLI commands

[mnriem]

Description

Refactor the specify bundle hierarchy to follow design/cli.md:

• move each real bundle command into a dedicated command_<name>.py module
• retain catalog/ as the only nested package because it is a genuine CLI namespace
• flatten bundle domain APIs into specify_cli/bundles/ while preserving the public BundlerError import compatibility boundary
• move command-focused tests into the mirrored tests/specify_cli/bundles/ hierarchy while retaining genuine contracts in their existing suites
• remove the obsolete grouped command module and nested implementation packages

The rebase preserves upstream additions including bundle add, first-party catalog fallback behavior, and offline bundled-workflow installation. User-visible help is byte-identical to upstream/main.

Testing

• Tested the complete specify bundle help surface locally and confirmed byte-identical output against upstream/main (36,645 bytes)
• Ran the complete repository suite: 8,357 passed, 16 skipped, 53 warnings (8,373 collected; upstream collects 8,372)
• Ran focused bundle and relevant cross-domain tests: 385 passed
• Ran uvx ruff@0.15.0 check src tests
• Ran git diff --check
• Built the wheel and verified every new command module is packaged and obsolete bundle modules are absent
• Verified command registration/order, compatibility imports, and no stale private import paths

AI Disclosure

• I did not use AI assistance for this contribution
• I did use AI assistance (fill in the disclosure below)

AI disclosure: GitHub Copilot, powered by GPT-5.6 Sol, operated autonomously for repository analysis, code and test refactoring, rebase conflict resolution, validation, and PR drafting on behalf of @mnriem. The code and PR description are fully AI-drafted; validation evidence was produced by local automated commands.

[Copilot]

Copilot review overview

🟢 Approval recommended

The structural refactor preserves registration and compatibility while retaining comprehensive command and domain regression coverage.

Review effort: Balanced
Findings: None

What changed in this PR

Reorganizes the bundle CLI to match the repository’s command architecture while preserving behavior and the legacy BundlerError import.

Changes:

• Splits bundle and catalog handlers into dedicated command modules.
• Flattens bundle domain services under specify_cli.bundles.
• Mirrors command tests and preserves regression and compatibility coverage.

File	Description
tests/​unit/​test_bundle_download_url.py	Moves source-resolution tests.
tests/​test_init_dir_cli.py	Relocates bundle-specific override tests.
tests/​specify_cli/​bundles/​test_yamlio.py	Updates flattened imports.
tests/​specify_cli/​bundles/​test_versioning.py	Updates flattened imports.
tests/​specify_cli/​bundles/​test_validator.py	Updates validator imports.
tests/​specify_cli/​bundles/​test_sources.py	Consolidates source-resolution regressions.
tests/​specify_cli/​bundles/​test_security_paths.py	Updates security-path imports.
tests/​specify_cli/​bundles/​test_resolver.py	Updates resolver imports.
tests/​specify_cli/​bundles/​test_references.py	Updates reference imports.
tests/​specify_cli/​bundles/​test_records.py	Updates record imports.
tests/​specify_cli/​bundles/​test_primitives.py	Updates primitive-service imports.
tests/​specify_cli/​bundles/​test_packager.py	Updates packager imports.
tests/​specify_cli/​bundles/​test_offline.py	Updates offline catalog tests.
tests/​specify_cli/​bundles/​test_installer.py	Updates installer imports and patches.
tests/​specify_cli/​bundles/​test_conflict.py	Updates conflict imports.
tests/​specify_cli/​bundles/​test_commands.py	Tests shared CLI registration and errors.
tests/​specify_cli/​bundles/​test_command_validate.py	Mirrors validate command coverage.
tests/​specify_cli/​bundles/​test_command_update.py	Mirrors update command coverage.
tests/​specify_cli/​bundles/​test_command_search.py	Mirrors search command coverage.
tests/​specify_cli/​bundles/​test_command_remove.py	Mirrors remove command coverage.
tests/​specify_cli/​bundles/​test_command_list.py	Mirrors list command coverage.
tests/​specify_cli/​bundles/​test_command_install.py	Consolidates install command coverage.
tests/​specify_cli/​bundles/​test_command_init.py	Mirrors init command coverage.
tests/​specify_cli/​bundles/​test_command_info.py	Consolidates info and download coverage.
tests/​specify_cli/​bundles/​test_command_build.py	Mirrors build command coverage.
tests/​specify_cli/​bundles/​test_command_add.py	Covers the add alias and catalog flow.
tests/​specify_cli/​bundles/​test_catalog_stack.py	Updates catalog-stack imports.
tests/​specify_cli/​bundles/​test_catalog_config.py	Updates catalog-config imports.
tests/​specify_cli/​bundles/​test_bundles.py	Verifies error-import compatibility.
tests/​specify_cli/​bundles/​test_adapters.py	Updates adapter imports.
tests/​specify_cli/​bundles/​helpers.py	Moves shared bundle test helpers.
tests/​specify_cli/​bundles/​conftest.py	Adds scoped project fixture.
tests/​specify_cli/​bundles/​catalog/​test_command_remove.py	Mirrors catalog remove coverage.
tests/​specify_cli/​bundles/​catalog/​test_command_list.py	Mirrors catalog list coverage.
tests/​specify_cli/​bundles/​catalog/​test_command_add.py	Mirrors catalog add coverage.
tests/​specify_cli/​bundles/​catalog/​__init__.py	Adds nested test package marker.
tests/​specify_cli/​bundles/​_command_helpers.py	Shares command-test setup helpers.
tests/​specify_cli/​bundles/​__init__.py	Adds bundle test package marker.
tests/​integration/​test_bundler_init_install.py	Moves install initialization tests.
tests/​contract/​test_manifest_schema.py	Updates manifest API imports.
tests/​contract/​test_catalog_schema.py	Updates catalog API imports.
src/​specify_cli/​commands/​bundle/​__init__.py	Removes obsolete monolithic CLI module.
src/​specify_cli/​bundles/​yamlio.py	Flattens package imports.
src/​specify_cli/​bundles/​versioning.py	Flattens package imports.
src/​specify_cli/​bundles/​validator.py	Flattens validator dependencies.
src/​specify_cli/​bundles/​sources.py	Extracts manifest source resolution.
src/​specify_cli/​bundles/​resolver.py	Flattens resolver dependencies.
src/​specify_cli/​bundles/​references.py	Flattens reference dependencies.
src/​specify_cli/​bundles/​records.py	Flattens record dependencies.
src/​specify_cli/​bundles/​project.py	Flattens project helpers.
src/​specify_cli/​bundles/​primitives.py	Flattens primitive integrations.
src/​specify_cli/​bundles/​packager.py	Flattens packager dependencies.
src/​specify_cli/​bundles/​manifest.py	Flattens manifest dependencies.
src/​specify_cli/​bundles/​installer.py	Flattens installer dependencies.
src/​specify_cli/​bundles/​conflict.py	Flattens conflict dependencies.
src/​specify_cli/​bundles/​command_validate.py	Implements validate CLI adapter.
src/​specify_cli/​bundles/​command_update.py	Implements update CLI adapter.
src/​specify_cli/​bundles/​command_search.py	Implements search CLI adapter.
src/​specify_cli/​bundles/​command_remove.py	Implements remove CLI adapter.
src/​specify_cli/​bundles/​command_list.py	Implements list CLI adapter.
src/​specify_cli/​bundles/​command_install.py	Implements install CLI adapter.
src/​specify_cli/​bundles/​command_init.py	Implements init CLI adapter.
src/​specify_cli/​bundles/​command_info.py	Implements info CLI adapter.
src/​specify_cli/​bundles/​command_build.py	Implements build CLI adapter.
src/​specify_cli/​bundles/​command_add.py	Implements add CLI adapter.
src/​specify_cli/​bundles/​catalogs.py	Flattens catalog models.
src/​specify_cli/​bundles/​catalog/​command_remove.py	Implements catalog remove adapter.
src/​specify_cli/​bundles/​catalog/​command_list.py	Implements catalog list adapter.
src/​specify_cli/​bundles/​catalog/​command_add.py	Implements catalog add adapter.
src/​specify_cli/​bundles/​catalog/​__init__.py	Registers nested catalog commands.
src/​specify_cli/​bundles/​catalog_stack.py	Flattens catalog-stack dependencies.
src/​specify_cli/​bundles/​catalog_config.py	Flattens catalog configuration.
src/​specify_cli/​bundles/​adapters.py	Flattens external adapters.
src/​specify_cli/​bundles/​_commands.py	Centralizes group infrastructure and registration.
src/​specify_cli/​bundles/​__init__.py	Documents the flattened package API.
src/​specify_cli/​bundler/​services/​__init__.py	Removes obsolete nested package.
src/​specify_cli/​bundler/​models/​__init__.py	Removes obsolete nested package.
src/​specify_cli/​bundler/​lib/​__init__.py	Removes obsolete nested package.
src/​specify_cli/​bundler/​commands_impl/​__init__.py	Removes obsolete implementation package.
src/​specify_cli/​bundler.py	Preserves legacy BundlerError import.
src/​specify_cli/​__init__.py	Registers the reorganized bundle CLI.

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