Long options for mpileup

(Feature branch and pull request created on behalf of @pd3.)

Mpileup has long used `getopt_long`, ever since the `--ff`/`--rf` options were added but no obviously good short option letters were available for them.  Petr added long equivalents of other mpileup options in eb2b30907ada8dc77b2d373dcf36ea6b8b9d64d2, but we need to come to consensus on some of the details before this is merged to **develop** --- see the commentary on that change and below.