Version:           3.4.1 (using KDE KDE 3.5.7)
Installed from:    Fedora RPMs
Compiler:          gcc (GCC) 4.1.2 20070626 (Red Hat 4.1.2-13) 
OS:                Linux

let me explain with an example:
say, I added some existing .cpp files from one directory, and where one of the files under that directory has the name 'minc_opengl.cpp'.
later when I add the contents of another directory, that happen to contain the same file name 'minc_opengl.cpp' but of course with different code in it, I end-up with only one file 'minc_opengl.cpp' of the latest directory (and later of course many linking problems).
I think there should be a warning of some kind to let me know about such situations (very common in large projects).