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
Traditionally, Eclipse assumes that the .project file is at the top-level directory of your project's sources and all the source code below it is included in the project. However, I think that you should be able to use linked folders so that you have a Eclipse project directory which is basically empty but for a .project file and a linked folder which points to your source tree. I do not think however that you can explicitly list the files to include in the project.
EDIT: if you do find a solution to this, please let me know.