The setup directory not only includes the scripts for the windows-installer, but also the files needed to integrate C::B in linux desktops.
That makes the debian-build (with dpkg-buildpackage) break.
One solution would be to remove the "usr/share/applications" entry from "debian/codeblocks.install", but that would also remove the "codeblocks.desktop", "codeblocks.xml " C::B-pixmap and menu-entries from the package what is not good I think.
The better solution is in my opinion to move the "mime"-directory (subdir of "setup") back to trunk and add the appropriate-entries to "configure.in" and "Makefile.am".