OS: Ubuntu 14.04 32-bit.
I've installed uisp, libusb, made some rules, and I can program my chip with avrdude with commandline. I'd like it to be programmed from Arduino IDE.
According to lsusb and dmesg, AVR MK II is recognized by the computer.
Why won't Arduino find it....?
Well I have no idea what an AVR MKII is, but if you mean an AVRISP MKII, it is not a USB serial device and so no port will show. Avrdude should have no problem working with it and you say it works from the command line. The Arduino IDE uses Avrdude so that should work also. Try it.
It is the AVRISP MK II:
Why does it not show in the Tools-> Serial Port menu? If I have to manually register it, where do I do that?
Its programmer not the port. for Board. If you goto tools-> programmer->(here you find AVR MKII)
Chose the programmer you have.
use any example code for arduino
For uploading code using programmer u need to goto file-> upload using programmer
I got a permission denied, so I started Arduino as root, and the upload completed with no errors.
I would be awesome to not have to run Arduino as root.