In the <arduino>hardware\tools\x86\bin directory (i.e. arduino-1.5.3\hardware\tools\x86\bin for the latest IDE) there is a sysimage_00782_capsulefull_noreset.cap 6.8MB file that looks like the firmware that is loaded via the IDE.
In the same directory there is also a update.sh that is probably called for the firmware update.
If someone could give some hints about the .cap file format and wether existing 0.9.0 cap file can be used, it could be just a matter of replacing the file and running an upgrade from the IDE.