sopt never displays full sub-command descriptions

[tfenne]

@nh13 It would appear that your latest refactor makes it so that sopt never prints out the full description for a sub-command from @clp(description="..."). This is true for both the cases where parseCommandAndSubcommand() is invoked (like in dagr) and the case when parseSubCommand() is invoked (like in fgbio). E.g. neither of the following print out the command/pipeline descriptions:

java -jar dagr.jar ExamplePipeline --help
java -jar fgbio.jar FilterBam --help

I took a look at fixing this myself and got lost in the logic around where you want things to show up when doing command/subcommand parsing vs. just sub-command parsing, and when extraUsage is and isn't provided. Can you take a look please?