Improve the documentation on `tap package` and `tap run`

1. Improve the contents of tap package -h and tap package <subcommand> -h, and align them with the Markdown documentation
2. Improve the contents of tap run -h, and align them with the Markdown documentation
3. Merge the Markdown documentation contained in
   • CLI Usage, and
   • CLI Reference
4. Remove CLI Reference fixing possible cross references (redirecting them to CLI Usage)