Okay, did as you say (thank you) but I have run into a error when i try to build "make cia" I get;
cloud@cloud-HP-Pavilion-tx2500-Notebook-PC:~/prboom3ds$ make cia
make[1]: Entering directory `/home/cloud/prboom3ds'
built ... /home/cloud/prboom3ds/prboom3ds.elf /home/cloud/prboom3ds/prboom3ds.cia
prboom3ds
arm-none-eabi-strip build_stripped.elf
/home/cloud/prboom3ds\resources\makerom -f cci -rsf /home/cloud/prboom3ds\resources\gw_workaround.rsf -target d -exefslogo -elf build_stripped.elf -icon /home/cloud/prboom3ds\resources\icon.bin -banner /home/cloud/prboom3ds\resources\banner.bin -o /home/cloud/prboom3ds\prboom3ds.3ds
make[2]: /home/cloud/prboom3dsresourcesmakerom: Command not found
make[2]: *** [/home/cloud/prboom3ds/prboom3ds.cia] Error 127
make[1]: *** [build] Error 2
make[1]: Leaving directory `/home/cloud/prboom3ds'
make: *** [cia] Error 2
So for kicks, after getting the feedback from above, I decided to copy the makerom out of the resources folder to /home/cloud/ and renamed makerom to prboom3dsresourcesmakerom as it was being called for but that gives me this error;
cloud@cloud-HP-Pavilion-tx2500-Notebook-PC:~/prboom3ds$ make cia
make[1]: Entering directory `/home/cloud/prboom3ds'
built ... /home/cloud/prboom3ds/prboom3ds.elf /home/cloud/prboom3ds/prboom3ds.cia
prboom3ds
arm-none-eabi-strip build_stripped.elf
/home/cloud/prboom3ds\resources\makerom -f cci -rsf /home/cloud/prboom3ds\resources\gw_workaround.rsf -target d -exefslogo -elf build_stripped.elf -icon /home/cloud/prboom3ds\resources\icon.bin -banner /home/cloud/prboom3ds\resources\banner.bin -o /home/cloud/prboom3ds\prboom3ds.3ds
[RSF ERROR] Failed to open /home/cloud/prboom3dsresourcesgw_workaround.rsf
make[2]: *** [/home/cloud/prboom3ds/prboom3ds.cia] Error 254
make[1]: *** [build] Error 2
make[1]: Leaving directory `/home/cloud/prboom3ds'
make: *** [cia] Error 2
soooo, I then thought it would be a good idea to copy the gw_workaround.rsf out of the resources folder to /home/cloud/ and renamed gw_workaround.rsf to prboom3dsresourcesgw_workaround.rsf as it was being called for but that gives me this error;
cloud@cloud-HP-Pavilion-tx2500-Notebook-PC:~/prboom3ds$ make cia
make[1]: Entering directory `/home/cloud/prboom3ds'
built ... /home/cloud/prboom3ds/prboom3ds.elf /home/cloud/prboom3ds/prboom3ds.cia
prboom3ds
arm-none-eabi-strip build_stripped.elf
/home/cloud/prboom3ds\resources\makerom -f cci -rsf /home/cloud/prboom3ds\resources\gw_workaround.rsf -target d -exefslogo -elf build_stripped.elf -icon /home/cloud/prboom3ds\resources\icon.bin -banner /home/cloud/prboom3ds\resources\banner.bin -o /home/cloud/prboom3ds\prboom3ds.3ds
[RSF ERROR] Unrecognised Key: 'Rom'
[RSF ERROR] Error Proccessing RSF file
make[2]: *** [/home/cloud/prboom3ds/prboom3ds.cia] Error 254
make[1]: *** [build] Error 2
make[1]: Leaving directory `/home/cloud/prboom3ds'
make: *** [cia] Error 2
I'm using Ubuntu. The makerom packaged with your release is makerom.exe so I instead compiled makerom from source and replaced it in the resources folder. Then I edited the Makefile and changed the two references to makerom.exe to makerom.
Any help would be appreciated

Sorry for the lengthy post.
Also, the .3dsx and .elf compiles just fine