run: Reorganizing option parsing, clarifying flags usage

We did miss the fact that a bunch of our new command
line flags were breaking -c usage, given that those
new flags parsed "only" filters to the existing cartesian
configurations.

So reorganize the general options parsing, and carefully
review which options can go with -c and which ones will
be ignored, documenting this on --help output.

This also resolves one of the requests from Igor Mammedov,
of not compulsorily setting --qemu-bin when using custom
config files. So if -c is provided and no --qemu-bin was
provided in the command line, no attempt to set it will
be made. Of course, that was also explained in the --help
output.

CC: Igor Mammedov <imammedo@redhat.com>
Signed-off-by: NLucas Meneghel Rodrigues <lmr@redhat.com>