Various hardcoded NUM_VARS which break when applied to diagnostics

[mirenradia]

There are several pieces of code that have NUM_VARS hardcoded which one might wish to use for diagnostics from #119 . Some of the ones I have found so far:

• https://github.com/GRChombo/GRChombo/blob/ffa4bbbda71f31453fcf532cb529e35ae15c4f7f/Source/BoxUtils/BoxPointers.hpp#L46
• https://github.com/GRChombo/GRChombo/blob/ffa4bbbda71f31453fcf532cb529e35ae15c4f7f/Source/BoxUtils/SetValue.hpp#L26
• https://github.com/GRChombo/GRChombo/blob/ffa4bbbda71f31453fcf532cb529e35ae15c4f7f/Source/BoxUtils/Cell.hpp#L104 and https://github.com/GRChombo/GRChombo/blob/ffa4bbbda71f31453fcf532cb529e35ae15c4f7f/Source/BoxUtils/Cell.hpp#L123 (and corresponding code in Cell.impl.hpp)
• Derivative.hpp has lots although I think derivatives of diagnostic vars shouldn't be taken in general since the outer boundary ghost cells are not filled (if not using periodic BCs).

[mirenradia]

Also we need to update the parameter files for some of the examples which still specify the asymptotic boundary values (in the case of Sommerfeld BCs) for variables which are now diagnostics.