Sync command reference with current CLI options

[rishabhsai]

Type of Change

• Bug fix
• New feature
• Breaking change
• Documentation update

Motivation and Context

The command reference still documents a registry scheme value the CLI no longer accepts. #2100 removed the auto scheme in code only, so all seven --scheme lines and the "Behavior of auto" block under container run disagree with container run --help, which prints One of (http, https) (default: https). #1744 added --kernel-arg to container run and container create without a reference entry, so grep -rn kernel-arg docs finds nothing. The shell completions note links to apple.github.io/swift-argument-parser, which now returns 404 for every path including its root, so it now points at the article's source in apple/swift-argument-parser, which returns 200. #1571 proposed a CI check to keep this file in sync with --help but was closed unmerged, so the drift is still here.

Testing

• Tested locally
• Added/updated tests
• Added/updated docs

Docs only. Compared each edited line against --help for run, create, image pull, image push, registry login, and machine create from a build of main, then checked grep -n "https, auto" docs/command-reference.md (no output), grep -c "default: https)" docs/command-reference.md (7), and grep -c "kernel-arg" docs/command-reference.md (2). container k8s create uses the same Flags.Registry group (ContainerK8s/Commands/K8sCreate.swift), so its line follows.

[github-actions]

Code Coverage

Tier	Line Coverage
Unit	24.88%
Integration	66.67%
Combined	76.08%