Redesign the `fgfa` command-line interface

[sampsyo]

Currently, the input and output file options are global options for the fgfa command. So you do stuff like this:

fgfa -i something.flatgfa stats

Instead of:

fgfa stats -i something.flatgfa

Or even:

fgfa stats something.flatgfa

As a purely cosmetic thing like that, this wouldn't be worth worrying about. But it actually causes a bunch of annoyance for the growing number of commands that don't read and/or write a variation graph. All these special cases are just to ignore the GFA/FlatGFA input arguments, for example, in cases where we don't need it:

pollen/flatgfa/src/cli/main.rs

Lines 67 to 84 in c243c6f

	// Another special case for parsing BED files,
	// since we do not parse a GFA file for that.
	if let Some(Command::BedIntersect(sub_args)) = args.command {
	cmds::bed_intersect(sub_args);
	return Ok(());
	}
	// Yet more special cases for sequence compression/decompression, which only
	// deal with raw sequence data and not GFA files.
	if let Some(Command::SeqExport(sub_args)) = args.command {
	cmds::seq_export(sub_args);
	return Ok(());
	}
	if let Some(Command::SeqImport(sub_args)) = args.command {
	cmds::seq_import(sub_args);
	return Ok(());
	}

Let's redesign the CLI so the input and output flags are per-subcommand.