Makefile can detect changes in alternate KFS dirs

If we don't have kfs-paths as the source of kern_initramfs_files, make
probably won't notice the change to files in any directory other than
FIRST_KFS_PATH, and thus it won't rebuild KFS with the updated files.

This change can detect missing directories too, though you'll need to
run make a couple times if you recently had a bad KFS paths list, due to
how we don't process the .config right away.