Improve documentation and `--help` in the context of SIP-46-related changes

[Gedochao]

Describe what needs to be done and why This is a catch-all ticket for docs and help improvements tied to our SIP

Related tickets #1309 #1308

To Do

• document all the behaviours tied to the default command (when scala-cli is called without explicitly passing a sub-command)
  • those should be at least broadly made clear in the relevant --help
  • a cookbook giving examples of all the less obvious behaviours would probably be useful
• document backwards compatibility with the scala command
  • in particular, all known incompatibilities which we won't fix should be documented (i.e. passing a main class as an input instead of the --main-class option)
• future-proof our docs website for post-SIP
• ... (probably more to come)