Fix CLI consistency report gaps

[WilliamK112]

Summary

Fixes #1968.

• add the missing apm doctor CLI reference page and link it from the reference index
• add missing existing commands to the reference index and fix the README CLI reference URL
• clarify config get, deps clean --yes, init --yes, and deprecated unpack help text
• add CLI help regression coverage for config get --help and the top-level unpack replacement summary

Verification

• uv run pytest tests/integration/test_wave4_cli_commands_coverage.py::TestConfigCommand tests/integration/test_wave6_deps_cli_coverage.py::TestDepsClean tests/integration/test_wave6_init_pack_coverage.py::TestInitBasic tests/integration/test_wave6_init_pack_coverage.py::TestPackBasic -q
• uv run ruff check src/apm_cli/commands/config.py src/apm_cli/commands/deps/cli.py src/apm_cli/commands/init.py src/apm_cli/commands/pack.py tests/integration/test_wave4_cli_commands_coverage.py tests/integration/test_wave6_init_pack_coverage.py
• uv run ruff format --check src/apm_cli/commands/config.py src/apm_cli/commands/deps/cli.py src/apm_cli/commands/init.py src/apm_cli/commands/pack.py tests/integration/test_wave4_cli_commands_coverage.py tests/integration/test_wave6_init_pack_coverage.py
• uv run apm --help
• uv run apm config get --help
• uv run apm deps clean --help
• uv run apm init --help
• uv run apm doctor --help
• git diff --check
• cd docs && npm ci && npm run build (passes; existing Astro/Vite warnings only, internal links valid)

Signed-off-by: WilliamK112 WilliamK112@users.noreply.github.com

[Copilot]

Pull request overview

Addresses gaps from the CLI consistency report (Issue #1968) by improving CLI help text consistency, adding missing CLI reference docs, and adding regression tests to keep help output aligned with docs.

Changes:

• Added/updated CLI help text for config get, deps clean --yes, init --yes, and improved the deprecated unpack top-level summary.
• Extended integration coverage to regression-test apm --help and apm config get --help output.
• Updated docs: added apm doctor reference page and expanded the reference index command table.

Reviewed changes

Copilot reviewed 11 out of 11 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
tests/integration/test_wave6_init_pack_coverage.py	Adds regression assertion that top-level help names the unpack replacement.
tests/integration/test_wave4_cli_commands_coverage.py	Adds regression assertion that config get --help documents list-all behavior.
src/apm_cli/commands/pack.py	Adds short_help for deprecated unpack to surface replacement in apm --help.
src/apm_cli/commands/init.py	Aligns --yes help wording with the consistency report.
src/apm_cli/commands/deps/cli.py	Aligns deps clean --yes help wording.
src/apm_cli/commands/config.py	Updates config get command help to mention omit-KEY list-all behavior.
README.md	Updates the “CLI Reference” link target.
docs/src/content/docs/reference/index.md	Adds missing commands (incl. doctor) to the reference index table.
docs/src/content/docs/reference/cli/init.md	Updates init --yes wording to match CLI help.
docs/src/content/docs/reference/cli/doctor.md	Adds the missing apm doctor CLI reference page.
docs/src/content/docs/reference/cli/deps.md	Updates deps clean --yes wording to match CLI help.