Thanks for emailing me a copy of your Wixel SDK. I was able to compile it just fine using make 3.82-pololu1. Here is the output:
However, when I tried to do "make clean" I got this error:
It looks like you've added so many apps that the number of arguments Make tries to pass to rm is way too large, so "make clean" probably wasn't actually doing anything for you. I've pushed a change up to the official Wixel SDK that fixes this problem (at least for now).
I also saw some very weird behavior from make (Interrupt/Exception caught at 0x416638) which seemed to be triggered by me running a command such as "make clean >error.txt" and seemed to be fixed sometimes by various odd actions such as closing the Command Prompt and reopening it. There is probably a bug in make and I will look into it.
In the meantime, as a workaround to the error you are having, I think you should comment out the "-include $(Ds)" line at the bottom of the Makefile. One side effect is that whenever you edit a header (.h) file you will have to run "make clean" afterwards to ensure that all the affected .c files get recompiled.
Here is the Makefile from your copy of the Wixel SDK, modified to have both of those changes in it (fixing make clean, commenting out the include line):
Makefile.txt (6.47 KB)
I recommend renaming this file to Makefile, replacing your existing Makefile with it, then running "make clean", then running "make". You should run those two commands at a Command Prompt instead of from within Eclipse so you can see any errors that might happen.