"salmon --help" is confusing

[tseemann]

I think something like this (like samtools, kallisto etc

salmon v0.6.0 - description here

Usage: salmon <COMMAND> [-h | options]

Commands:
    index         Create a salmon index
    quant         Count blah
    swim          Whatever

would be much clearer than the current help

salmon --help
Allowed Options:
  -v [ --version ]      print version string
  --no-version-check    don't check with the server to see if this is the
                        latest version
  -h [ --help ]         produce help message

    Salmon v0.6.0
    ===============

    Please invoke salmon with one of the following commands {index, quant, swim}.
    For more information on the options for these particular methods, use the -h
    flag along with the method name.  For example:

    salmon index -h

    will give you detailed help information about the index command.

[rob-p]

This is fixed in c5d4a23