Just comment out the file which does not exist (e17/buildlink3.mk).
Add avr-gdb, and partly sort.
+SUBDIR+=	avr-gdb

-SUBDIR+=	mpc-el
 SUBDIR+=	mpb-openmpi
+SUBDIR+=	mpc-el

-SUBDIR+=	mupen64plus-extraplugins
 SUBDIR+=	mupen64plus
+SUBDIR+=	mupen64plus-extraplugins