Improve command-line handling and documentation

In particular:

- generally improve the look of the man page and help message
- add missing command line options to the man page
- reorder command line options to be more consistent
- use the same order for command line options everywhere (man page, code, help message)
- add missing switches in getopt_long call (-M, -F)
- fix incorrect switch in getopt_long call (-Z)

Note that a few options were never documented (they are now marked as
"MISSING" in the man page).