We have a topdirectory containing code for lots of different projects. I would like to create an Eclipse CDT-project that contains only the source needed to work on and compile
In Eclipse, you can selectively import certain directories to be included in the project.
You can create an eclipse project somewhere else in your drive, and then create links only to the folders that you want in your original location (these are called "linked resources" in Eclipse)
You can also use the linked resource strategy for an entire project (I mean an Eclipse project, not your top-level project). For example, if your folder hierarchy is as follows:
/top-level
/top-level/projectA
/top-level/projectA/subProjectA
/top-level/projectB
You can create an eclipse workspace at location /my-workspace, create a project called subProjectA and have it linked to /top-level/projectA/subProjectA. You can do the same for projectB and they will appear in your Eclipse workspace as if they are side-by-side in a flat hierarchy.