Big cleanup of RunTest and references

Hi John,

I did a overall cleanup of RunTests.  It is now easier to debug: there's a new -v <level> verbose option, it no longer spews minor comments like "reference is empty ... ignored" unless -v 1 is passed.  Also a bit of refactoring and a few better messages.

I also removed multiple *.stdout references where the refs were empty.

Most importantly: after Vaclav found the -W <width> bug when calling 'diff --side-by-side' in RunTests which was sometimes truncating the least significant digits on some lines, and also after accounting to the %6g vs %4g formats of the average loss and weighted sum numbers, I realized at least some of the "minor (<0.001) precision differences ignored" would no longer happen at least on the same architecture, if we simply update the references to agree with what the latest code prints.  Although I still see many in the 32-bit build (Travis).

It makes the test-suite run a bit faster and its output is cleaner on 64-bit now.