So I've found the files I want to include, they are in (on Linux) /usr/avr/include/avr/ so I tried doing a softlink from <ArduinoHome>/hardware/tools/avr/avr to /usr/avr/include/avr.
I've just encountered a problem similar to this (on my fresh install of Debian 5/Lenny) and fixed it by installing the following:gccgcc-avravr-libcavrprogavrdudeSome of those probably don't need to be installed but I just installed the lot and it seems to work.
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