Adaptations to preprocessing

[stilscher]

This PR includes

• some fixes for the preprocessing with cilly make
• some changes in the preprocessing using a compilation database that were required for goblint/bench@#17. In the compilation database of this project, sometimes the -o option was not included in the arguments explicitly and so the preprocessing in Goblint failed. Since the generated compilation database generally looked fine to me and I couldn't find anything about the option -o being a required option in the arguments, I decided to extend the preprocessing in Goblint to handle this case.

[sim642]

This will conflict with #587, so I don't know if there's any preference which one should be merged first.

[sim642]

I fixed the merge conflict myself.