The archive has a main folder Firmwares_WindowsDrivers_AVRISPMK2 with three sub-folders:

AVR-ATMEL-STUDIO - contains hex file that can be uploaded to the programmer via the USB and Atmel Flip 

AVR-DUDE-LINUX - contains hex file that can be uploaded to the programmer via the USB and Atmel Flip

AVR-ISP-MK2-DEFAULT-ELF - contains default AVR-ISP-MK2 elf, you need a programmer to upload it to the AVR-ISP-MK2 - helpful if you corrupted the bootloader; you would also need to carefully open the case and change the position of the PTH jumper ER/PGM; after programming switch the jumper back to default position. The whole programming is done using the ICSP10 connector. Please note that opening the case voids the warranty.

Instructions on how to install the latest firmware or get support for Linux might be found at the AVR-ISP-MK2's web page at Olimex's web-site. Refer to the user manual for step-by-step instructions.

The firmwares had been tested and confirmed working with Atmel Studio versions up to v6.2, and AVRDude versions up to v6.1. Windows versions up to Windows 8.1 were used. Several Linux distributions were also tested and no problems were found.

Changelog:

10.05.13 - added support for Atmel Studio v6.1
28.08.14 - added default elf file in the archive