Fix bug using replaceOptAln
Fixing geometry bugs

Replacing broken methods with RotationAxis.getProjectedDistance()
Check that SymmRefiner's hard-coded path exists

Its the next best thing to actual arguments
Improving robustness of NamesCensus input file

Allow comments and trailing tokens in the domain list, allowing the
benchmark.tsv file from the supplementals to be used.

Also stores the mapping in the results file
Fix logging configuration

remove duplicate console appenders & separate test and main
configurations
Use predictable scop version
Fix bug with calculating order of translational repeats
Adding test for RotationOrderDetector
Adding second detection method within RotationOrderDetector
Adding some additional RotationOrderDetector methods
Adding cusp code
RotationOrderDetector features

* Added additional methods, which can be selected through an enum
  * Harmonic series, with either fixed or floating intercept
  * Single sin^2 or cusp functions, optimizing either amplitude or SSE
* Strong command line interface
Resolve conflicts. Added sampleRotations().