The mentioned project itself has about 3,5k class-Files with a total size of about 25MB. If this is relevant, it has a lot of dependencies.
I looked through the logs of eclipse from the past ten days and didn't find anything what could cause this. But I'm pretty sure I had problems with this in the past ten days.
Because the CDI Tools 4 are at Alpha state and we need those tools in a different project I'm not convinced to switch versions. I deactivated CDI tools for this project. I will keep an eye on the progress bar to find out if eclipse invokes the builder for this project again.