If the files are coming from a CVS repository, as is usually the case, then they will be RCS files. These have a `,v' suffix which must be taken into account in the patterns. For example, the FreeBSD documentation files are in a sub-directory of base called `doc'. If `Makefile' from that directory is not required then the line doc/Makefile will not work because the file on the server is called Makefile,v.' A better solution would be doc/Makefile* which will match whether `Makefile' is an RCS file or not.
Assuming you want the most recent version of the sources, you simply need to add "tag=." to your supfile.