Warnings and errors

[illorenzo7]

I don't think the code is consistent in its usage of warnings and errors. I believe a "warning" should occur when the code notices something might be up, and prints a useful message, but keeps running. If there is an "error", the code should exit. Currently lots of "errors" don't lead to exits. It looks like most of these occur in the (relatively new) files:

PDE_Coefficients.F90
and
Generic_Input.F90

I'm not sure of best way forward: Either we make the errors that don't lead to exits warnings, or we force the things listed as errors to exit. It might be worth going through the cases in the above files one by one. I plan to do this for PDE_Coefficients after addressing the custom reference stuff: #419 and #420.

I'm flagging this as a "bug" as well as "errors and messages" because the code isn't running as it should in some cases. That could be a little harsh though...