Al B
To fix this issue all you need to do is remove the IOIOLib module
- Right click on project
- Select "open module settings" at the bottom
- select "IOIOLib" in the module list
- Click the "-" minus to remove
and change the dependency to the IOIOLibAndroid (../IOIOMAnager/build.gradle)
change the "compile project(':iOIOLib')" in the dependencies to "compile project(':iOIOLibAndroid')"

Notice "IOIOLib" is still listed in the project but it is not in bold like the others
Ytai
Android Studio may be in beta, but it is an incredible improvement over the Eclipse/ADT solution. You should really give it a shot. Also, I was able to use this with the Nexus 5 via blue tooth, but not via direct connect. Is there something I can do to make this work (via source changes) or is the Nexus 5 OTG support not compatible with the existing legacy IOIO hardware (Sparkfun 16)
All
If you are having difficulty flashing using Nexus 5 IOIO via USB try via blue tooth. Some old version of the firmware won't show up as target devices from Nexus 5, I had to use an old my touch G3 via USB to flash the updated ROM.
Hope this helps.