CLI sort: remove unneeded imports
CLI sort: remove dead writes
CLI sort: note the sort order in --help output
Twiddle whitespace
CLI: implement 'fixmate', like samtools fixmate
CLIPlugin: rename optionDescs field

It was a bit confusing to have the same name for the instance-specific
one and the static ones defined separately in each plugin.
CLI: refactor commonalities into CLIMR{,BAM}Plugin

This isn't all-inclusive: some copy-pasted things still remain, such as
the SAM/BAM merging done in both fixmate and sort.

Fixes an error in SummarySort: it used to have an "output-dir" option
when it was supposed to be "output-file".

Now everything is unified to use "output-merged-path", bumping all
affected plugin versions by 0.1, with the exception of the unreleased
fixmate plugin.
CLI: move basic reducer output merging into Utils

Turning four mostly-copies of this code into just one.
CLI: move header merging functionality into Utils
CLI: move SAM/BAM output merging into Utils
CLI: refactor common SAM/BAM output formats
Merge remote-tracking branch 'upstream/master'