Move -nice handling to CommandLineModuleManager

Now also the tools written using the C++ framework support the -nice
command-line option.  The system also behaves more consistently, as now
all programs except mdrun and gmx-view default to -nice 19.  Previously,
there was no really consistent logic for where PCA_BE_NICE was set and
where not.

Remove PCA_BE_NICE as it is no longer used.  parse_common_args() no
longer has any options that it unconditionally adds, which completes one
step in full migration to the wrapper binary.

Change-Id: I35a464d3263bc20e98ad1d381e93fdc2749931a2