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Fix 1 adds a new makefile that allows full dynamic linking on Linux. This is the only way pic32prog is able to build on my system.
Fix 2 adds the DTR|RTS toggle on serial for any non-windows OS. This fixes the problem with detecting the UNO32. I don't have windows, but the fix is similar, therefore I have not included it as a patch. However code that should work will look something like this:
Hope this helps.