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I'm pretty sure the upgrade is the cause of the problem
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After compiling the Arduino SDK, can you run it at /opt/ucc/micros/arduino/arduinoSDK/build/linux/work/arduino ?
I have my desktop file installed in $HOME/.local/share/applications. So this is valid for my user only. Installing it in /usr/share/applications make is usable system wide.
An easy way to generate the .desktop file is to run the program,in which case the icon should come up on the Unity task bar. Then you can fix it there right clicking the icon and selecting "lock to launcher".
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