Ben Collver wrote:
> The Debian package system just has a single file containing all the
> differences from the official program distribution.

This single diff is only for the source package as a whole.  In 
practice, all patches go into debian/patches directory.  One of the 
alternative systems for handling patches in Debian packages is 
dpatch[1].  Other is part of the newest build system in Debian CDBS[2].

[1] 
http://cvs.alioth.debian.org/cgi-bin/cvsweb.cgi/dpatch/README?cvsroot=dpatch
[2] http://build-common.alioth.debian.org/
 
http://cvs.alioth.debian.org/cgi-bin/cvsweb.cgi/cdbs/?cvsroot=build-common

Regards
-- 
Ognyan Kulev <ogi@{fmi.uni-sofia.bg,fsa-bg.org,jabber.org}>
7D9F 66E6 68B7 A62B 0FCF  EB04 80BF 3A8C A252 9782