When processing the flags for -h/--help and -v/--version, only check
the flags in checkVersion() and checkHelp() instead of also printing
the associated message.
This fixes the problem of `app -h` and `app -v` printing their output
twice. The doubling was caused by printing the message once for each
registred alias for the given flags (-h/--help and -v/--version).
Resolves#285
