scripts: define SYSTEM and CONFIGDIR

instead to use always /usr as default prefix and /etc as default configdir
SYSTEM and CONFIGDIR variables are defined inside the main Makefile and project.mk uses them
scripts: uses SYSTEM and CONFIGDIR variables inside Makefile(s)
init: set SYSTEM and CONFIGDIR with configuration variables

make menuconfig allow to set SYSTEM and CONFIGDIR
for lsb tree SYSTEM is defined as "usr"
for android tree SYSTEM is defined as "system"
for the both CONFIGDIR is defined as "etc"