Arduino has released a major update to their toolset, now version 1.6.0. It includes better support for the ARM type Arduino CPUs and is now the 'primary' release stream. Of impact to the Arduino Alternator Regulator is this release also has updated the GCC compiler - resulting in about a 5% reduction in code size!
But they have also changed some of the file structures with regards to enabling custom bootloaders.
If you look under the Arduino Libs resource tab above you will see a new folder to support the Arduino IDE 1.6.0 with a fixed Optiboot to allow the watchdog to function (as opposed to totally wedge the system using the as-included 8Mhz bootloader in the Arduino IDE). Just follow install the new Arduino IDE release 1.6.0, copy down the files from the resource tab above and follow the instructions in the readme.txt file to allow the newest Arduino development environment to support the improved bootloader for 8Mhz operating of an ATmega328p cpu.