I got my nice Atmel in-system-programmer today, but unfortunately, the Arduino IDE on Linux couldn’t use it to burn a bootloader to the MCU.
The fix for this was to create a new file /etc/udev/rules.d/99-avrispmkii.rules with the following line:
BUS=="usb", ACTION=="add", SYSFS{product}=="AVRISP mkII", MODE="0666", SYMLINK+="avrdev"
After a udev restart and re-plugging the ISP, the device node was world writable and the Arduino IDE could do its magic.