I have a C project in Eclipse that stores its files in two directories at the same level along with a bunch of other stuff that I do not need to have in the project.
/path/
/code_I_want
/bad_stuff/
/more_code_i_want/
/huge_pile_of_other_code/
Edit: The source directory is a Clearcase VOB mount point so I can't control what ends up there.