Automatic manapge generation with vg help --man

[faithokamoto]

Changelog Entry

To be copied to the draft changelog by merger:

• vg help --man will output a fully formed Markdown manpage
• vg help subcommand will output the same thing as running vg subcommand, i.e. the default helptext

Description

BEHOLD MY WORKS. Ahem. Extension of #4979 but now the Better (TM) manpage is generated by vg help --man instead of a separate script. I've diffed it against the current manpage and what changed were:

• A few subcommand blurbs were edited to be better (e.g. vg giraffe's dropped the "short" from before "read alignment")
• Things are correctly alphabetized
• Deprecated subcommands still have their helptext printed, they're just not in the lists at the top.

Because vg help now needs to be able to print helptexts for other commands, I have Subcommands save a helptext function. Some subcommands' helptext functions require extra arguments. I worked around this by defining extra standard-argument functions, e.g. see help_augment_default().

The main thing I'm worried about here is vg giraffe. I did some terrible no good very bad hacks to make its default helptext function work because the previous one really wanted to be passed a list of presets. If you have a better way to do that I'm all ears.