Created base GeomConfidence and StatConfidence protos

Created Log-ratio and Mahalanobis transformations for GeomConfidence calculation

Created Some documentation.
Minor changes to some theme convenience functions, they were not working when adding to gg object, since, the call for theme_update() was pulling an unupdated themeset.
Completed geom-confidence
Merge pull request #4 from nicholasehamilton/ConfidenceRegions

Confidence regions