Make help more helpful

[bmesuere]

Add more help to the help command, based on bmesuere/unipept#257

This blocks the 1.0 release (#5)

• cri issues
  • single newlines are filtered from the description.(Allow the use of single newlines in help output denisdefreyne/cri#38)
  • options help doesn't format the line width (Reflow long option descriptions denisdefreyne/cri#36)
  • no way to indicate that an option takes an argument (Make option requiredness more clear denisdefreyne/cri#37)
• peptfilter: shorthands for options are different
• unipept
  • display help when bare unipept command is run (show help when running the commands without parameters unipept#305)
  • -a should be a flag, not an option
• unipept pept2prot
• unipept pept2taxa
• unipept pept2lca
• unipept taxa2lca
• unipept taxonomy
• unipept config
  • add more info about where the settings are saved
  • add a list of available config options

Original pull request by @bmesuere on Fri Aug 15 2014 at 17:21.
Merged by @bmesuere on Wed May 20 2015 at 17:05.

[bmesuere]

@tvwillem can you confirm that the first 3 items in the todo-list are indeed cri issues?

Original comment by @bmesuere on Fri Aug 15 2014 at 17:49.

[bmesuere]

The --extra option in unipept pept2prot was changed to --all, so the version number should be bumped when this branch gets merged.

Original comment by @bmesuere on Fri Aug 15 2014 at 19:14.