We have a set up with 2 project, 1 main and 1 subproject, they are Java projects. They are all under the same directory.
Here is how the directory structure looks like :
Ok, in case this is useful to someone, I finally got this working with actually removing (git rm) the .claspath file. It was in the .gitignore, but for some reason, it seems it had been comitted at some point and was playing around.
After doing this and re-importing the projects in Eclipse everything went back to normal.
Thanks to the ones who tried to help.