Removing CE-specific parameters from the default CLI
Incrementing version numbers for StructureAlignments
Consolidate structure alignment -help handling

printHelp() is now required for all UserArgumentProcessors
(moved from it's previous location in StructureAlignment.)
This allows -h, -help, and -version to be handled consistently
in the argument parser rather than in each aligner.

Also cleaned up some 'throw Exception/catch Exception' uses.

Finally, slightly changed the behavior of boolean arguments. Valid
values are nothing (determine value based on '-no' prefix), t/true,
and f/false. Other options give errors rather than defaulting to
false (the Boolean.parseBoolean() behavior).
Adding runCECP.sh to the protein comparison bundle
Fixing CLI wrapper scripts