Ok, my application that I am porting has multiple directories and multiple sub-directories with multiple arches.
My next step is to take this simple app example provided by google.
steven@Steven:~/Downloads/NaCl/naclports/src/qemu/pnacl_qemu-0.9.1/qemu-2.2.1$ ls -al x86_64-softmmu/
total 31184
drwxr-xr-x 7 steven steven 4096 Jul 20 13:38 .
drwxr-xr-x 111 steven steven 16384 Jul 21 18:34 ..
-rw-r--r-- 1 steven steven 29533 Jul 20 13:37 arch_init.d
-rw-r--r-- 1 steven steven 131744 Jul 20 13:37 arch_init.o
-rw-r--r-- 1 steven steven 21857 Jul 20 13:37 balloon.d
-rw-r--r-- 1 steven steven 39352 Jul 20 13:37 balloon.o
-rw-r--r-- 1 steven steven 18209 Jul 20 13:37 bootdevice.d
-rw-r--r-- 1 steven steven 49216 Jul 20 13:37 bootdevice.o
-rw-rw-r-- 1 steven steven 1656 Jul 8 21:09 config-devices.mak
-rw-rw-r-- 1 steven steven 1656 Jul 8 21:09 config-devices.mak.old
-rw-r--r-- 1 steven steven 321 Jul 20 09:21 config-target.h
-rw-r--r-- 1 steven steven 321 Jul 20 09:21 config-target.h-timestamp
-rw-rw-r-- 1 steven steven 285 Jul 20 08:56 config-target.mak
-rw-r--r-- 1 steven steven 18328 Jul 20 13:37 cpu-exec.d
-rw-r--r-- 1 steven steven 82816 Jul 20 13:37 cpu-exec.o
-rw-r--r-- 1 steven steven 23831 Jul 20 13:37 cpus.d
-rw-r--r-- 1 steven steven 178048 Jul 20 13:37 cpus.o
-rw-r--r-- 1 steven steven 19146 Jul 20 13:37 cputlb.d
-rw-r--r-- 1 steven steven 205152 Jul 20 13:37 cputlb.o
-rw-r--r-- 1 steven steven 19421 Jul 20 13:37 device_tree.d
-rw-r--r-- 1 steven steven 60160 Jul 20 13:37 device_tree.o
-rw-r--r-- 1 steven steven 19409 Jul 20 13:37 disas.d
-rw-r--r-- 1 steven steven 70272 Jul 20 13:37 disas.o
-rw-r--r-- 1 steven steven 22058 Jul 20 13:37 dump.d
-rw-r--r-- 1 steven steven 181912 Jul 20 13:37 dump.o
-rw-r--r-- 1 steven steven 24466 Jul 20 13:37 exec.d
-rw-r--r-- 1 steven steven 313168 Jul 20 13:37 exec.o
drwxr-xr-x 2 steven steven 4096 Jul 20 13:37 fpu
-rw-r--r-- 1 steven steven 21499 Jul 20 13:37 gdbstub.d
-rw-r--r-- 1 steven steven 203256 Jul 20 13:37 gdbstub.o
-rw-r--r-- 1 steven steven 23354 Jul 20 13:37 hmp-commands.h
drwxr-xr-x 17 steven steven 4096 Jul 20 09:21 hw
-rw-r--r-- 1 steven steven 17783 Jul 20 13:37 ioport.d
-rw-r--r-- 1 steven steven 52888 Jul 20 13:37 ioport.o
-rw-r--r-- 1 steven steven 25320 Jul 20 13:37 kvm-all.d
-rw-r--r-- 1 steven steven 284696 Jul 20 13:37 kvm-all.o
lrwxrwxrwx 1 steven steven 90 Jul 20 08:56 Makefile -> /home/steven/Downloads/NaCl/naclports/src/qemu/pnacl_qemu-0.9.1/qemu-2.2.1/Makefile.target
-rw-r--r-- 1 steven steven 19821 Jul 20 13:37 memory.d
-rw-r--r-- 1 steven steven 17019 Jul 20 13:37 memory_mapping.d
-rw-r--r-- 1 steven steven 47560 Jul 20 13:37 memory_mapping.o
-rw-r--r-- 1 steven steven 358944 Jul 20 13:37 memory.o
-rw-r--r-- 1 steven steven 34933 Jul 20 13:37 monitor.d
-rw-r--r-- 1 steven steven 767672 Jul 20 13:37 monitor.o
-rw-r--r-- 1 steven steven 22639 Jul 20 13:37 numa.d
-rw-r--r-- 1 steven steven 64864 Jul 20 13:37 numa.o
-rwxr-xr-x 1 steven steven 27461128 Jul 20 13:38 qemu-system-x86_64
-rw-r--r-- 1 steven steven 15181 Jul 20 13:37 qmp-commands-old.h
-rw-r--r-- 1 steven steven 20432 Jul 20 13:37 qtest.d
-rw-r--r-- 1 steven steven 119472 Jul 20 13:37 qtest.o
-rw-r--r-- 1 steven steven 24388 Jul 20 13:37 savevm.d
-rw-r--r-- 1 steven steven 162816 Jul 20 13:37 savevm.o
drwxr-xr-x 2 steven steven 4096 Jul 20 13:38 target-i386
drwxr-xr-x 2 steven steven 4096 Jul 20 13:37 tcg
drwxr-xr-x 2 steven steven 4096 Jul 20 13:38 trace
-rw-r--r-- 1 steven steven 18738 Jul 20 13:37 translate-all.d
-rw-r--r-- 1 steven steven 108056 Jul 20 13:37 translate-all.o
-rw-r--r-- 1 steven steven 20800 Jul 20 13:37 xen-common.d
-rw-r--r-- 1 steven steven 64160 Jul 20 13:37 xen-common.o
-rw-r--r-- 1 steven steven 27304 Jul 20 13:37 xen-hvm.d
-rw-r--r-- 1 steven steven 161104 Jul 20 13:37 xen-hvm.o
-rw-r--r-- 1 steven steven 21457 Jul 20 13:37 xen-mapcache.d
-rw-r--r-- 1 steven steven 52752 Jul 20 13:37 xen-mapcache.o