Compile with extra warnings turned on. And more makefile/code tidying up.

This turns on most gcc warnings, and removes some unused variables and other code that triggers warnings.
Exceptions are:
-Wno-sign-compare : triggered by lots of comparisons of signed integer to foo.size(), which is unsigned.
-Wno-char-subscripts : triggered by the convert-to-hex functions (I may fix this in a future commit).