I filed an issue on this also, but the system allowed me to do it without logging in first and I can't find it. At any rate, perhaps it will be helpful here.
I was presented with the "Update Info" dialog when I started IDEA this morning, offering an upgrade from 12.1.2 -> 12.1.3. I clicked the "Update and Restart" button, and it's appearance changed to reflect the click. After that, nothing responds on that dialog or the IDE except the "minimize" widget. It's been in this state for about an hour.
I'd prefer not to kill IDEA, since my system crashed recently and when that happened IDEA's config files were corrupted, which took a good bit of time to fix (reinstall and reconfigure project).
According to Visual VM profiling, IDEA has two threads consuming almost all the CPU time:
I'm running on Linux Mint 14 with Oracle jdk1.6.0_45.
Does anyone have any advice other than "kill -9"?
Thanks for looking!