Remove #ifdef HAVE_CONFIG_H blocks, always rely on config.h

Continue sorting system includes and un-#ifdef'ing a few additional headers.
(HAVE_STRING, HAVE_UNISTD, HAVE_LIMITS, HAVE_PTHREAD).

Unconditionally define _GNU_SOURCE when used. Should audit use of this further
and possibly define this in config.h directly along with POSIX macros.

Remove last vestige of src/common/malloc.[ch].