Several bugfixes

-Fixed bug where failed linking would still return an exit code of 0
-Fixed bug where libraries always showed as nonexistent when compiling
with the gold linker
-Fixed some bugs in determining whether or not to recompile something,
particularly (but not solely) in the case of precompiled headers
-Some reorganization (will be a lot of this gradually happening as the
project moves forward)
-Changed a couple of errors to warnings