Better separate argument parsing from validation & post-parsing work

[Eyal Rozenberg]

We currently have a huge single function, parse_command_line_initially(), which does too many things. Specifically, it does post-parsing work:

• Checks for file existence.
• Validates GPU device availability.
• Sets the log level <- Kind of tricky, since we would like to apply the log level to the parsing of arguments...

Let's try to refactor this stuff out.

[Eyal Rozenberg]

This is basically done, I think.