Remove trailing whitespace
Remove stuff that doesn't make any sense
Fix screwing up build type flags.

The description of the build type was wrong,
and none of this stuff needs to be set up anyway.

Check the warning flags before adding.

Don't use -mtune=native by default, since that will
probably end in tragedy for someone.
Fix typo for required flags in hashmap/set checks
Enhance warnings
Check for flex and bison
Fix build in C++11 mode
Fix a large number of -Wignored-qualifiers