- php: add serve flags, packages subcommands, all commands
- pkg: fix description (GitHub repos not Go modules), add --add flag
- setup: replace --path/--ssh with --dry-run/--only
- doctor: add --verbose flag
- test: full documentation with all flags and JSON output
- Cleaned up TODO.md
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Generated by comparing `core --help` output against docs.
Lists missing commands, flags, and discrepancies.
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>