Better error messages for command line problems

[mooreryan]

Example is when you pass

-o some_dir -no-check-chimeras

you get

Error: option '-o' specified multiple times.
Try --help for help.

This behavior is correct, but doesn't help the user much. Not sure if I can make a better message or not without fiddling around with Trollop lib though.

[seanmcallister]

Why don't you just add to the error output something like "Check that long form options are headed by a double dash "--" instead of a single dash, which may lead to this error."?