After taking a better look at some documentation related to cdt (c/c++ development plug-in to eclipse) I found a way to use the makefile in the Photovore v1.zip. Now I can compile the code and program the robot with my Linux environment.
And just in case someone else is also interested to do some development work on Linux here's short instructions to get you going (on Ubuntu/Kubuntu).
1. Install binutils and gcc compiler for avr
> sudo apt-get install gcc-avr
2. Install avr-libc
> sudo apt-get install avr-libc
3. Install avr debuger
> sudo apt-get install gdb-avr
4. Install the programmer. I use uisp, but you can install your favorite tool
> sudo apt-get install uisp
That's it, now you have the basic avr tools installed. Next thing is to install Eclipse and a java runtime environment. The easiest way to do that is to use Adept, just select java and eclipse from the lists and press install.
5. start Eclipse as superuser and install cdt plug-in according to the instructions at http://max.berger.name/howto/cdt/cdt.pdf
6. start C/C++ Perspective and create a new "Standard Make C Project". This means that you are using an external make file, instead one created by Eclipse. This was my problem.
7. Use "Import" to bring c- and header files and the makefile to the project.
8. Compile and use your favorite tool to program the MCU.
I'm really happy to get this working and I hope my struggle will help someone else out there.