Cleaning up ScanSCOPForSymmetry

* Improved variable names
* Made Runnable (already implemented methods)
Adding refinement option to CeSymm
Allow algorithm to be changed for Census
Removing doRefine properties in favor of custom algorithms

Rather than propogate a doRefine flag through the census classes,
just create a new AlgorithmGiver that sets the CeSymm RefineResult property.
Fixed Log4J configuration (wrong package name).
Set ScopFactory to 1.75B in CESymmGUI.
Created temporary guessOrder() method.
Worked on Axis.guessOrder().
Made gradient, minimum metric change, and max symmetry order parameters.
Don't store AFPChain since it takes too much memory. Will need to do
something else for web version.
Made a no-argument Axis.guessOrder() method.
Allow buildDefault() to take an AlgorithmGiver.
Changed TM-score cutoffs back to 0.4.
Wrote generallySymmetricSmart() and generallySymmetryFromAngle().
Use code now in biojava-structure.
Wrote header comments.
Fixed a NPE.
Made work with changes to AstralScopDescriptionCensus and Astral in
biojava-structure.
Made work with PrintWriters, and wrote a nice header comment.
Changed TM-score cutoff to 0.4, and wrote nice header comments.