I'm attempting to compile and package Glibc for what may eventually become my own Linux distribution. --with-headers=directory allows me to tell Glibc that the kernel headers are in a different place. But how do I tell Glibc to put it's own headers in a non standard location?
if you run ./configure --help, it'll show many flags to control various install paths. for headers, use --includedir=/some/other/path.