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.
We need to change to: Takes index = 0, 1, 2