Creating DetectOrder demo program

This contains all the UI/main code from the RotationOrderDetector.
Run with -h for help info
Adding CeSymmMain for the main executable.
Changing CeSymmMain options

* Better default output format
* Accepts multiple structures
Adding Order detection & Significance options for CESymm

Any OrderDetector can be used for calculating order.

The SignificanceFactory is responsible for building a Significance
object. However, this isn’t currently displayed or used.
Merge remote-tracking branch 'dmysersturnbull/master'
Fixing default order method
CeSymm changes [Potential Conflict]

Adds the iSSignificant() method.

Incorporates some CeSymm changes from dmyersturnbull/biojava/master (2c2dca52).
These could potentially cause a conflict with a future biojava version.
If so, this commit can probably be ommitted.
Adding options to CeSymmMain for significance and order detection.
Adding names to CeSymmMain displays
Reordering dependencies to use the correct commons-cli version
Adding version info to Manifest
Moving CeSymmMain to symmetry-tools

https://github.com/rcsb/symmetry-tools
Removing commons-cli dependency
Merge branch 'moreoptions'

This branch added a number of command line options to CeSymmMain.
However, CeSymmMain was moved to symmetry-tools, so this merge is
mostly to preserve the commit history.