Change or deprecate  setValue and getValue in RankTwoTensor

This PR deals with the non standard signature of ```setValue``` and the non-standard one-based indexing (also in ```getValue```) as reported in #3485.

Just changing the signature would probably lead to warnings only (switching ```Real``` and ```unsigned int```). So the first step is making these methods private and see what errors pop up.
For these tensor reporter aux kernels, we'll have to probably have to change some tests and input files.  We'll definitely have to notify the user base since I know these reporter aux functions are being used by others.