Fix --enable-debug regression while still enabling overridable CFLAGS.

AC_PROG_CC sets some default values for CFLAGS on some systems, so
we need to separate between those, and flags that are passed in from
the command line.
Merge pull request #1405 from kacfengine/overridable_CFLAGS

Fix --enable-debug regression while still enabling overridable CFLAGS.