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dfu-util needed to be set as executable on OSX (Arduino board support v0.3.1)
I burned the bootloader using Arduino board support v0.3.1, and found I needed to chmod dfu-util. It was set to 0644, I set it to 0755.
After that I was able to flash the bootloader successfully.
@tangesazen Wait what did you do?
In the board support, dfu-util was set to 0644 (not-executable). Setting it to 0755 allowed it to run.