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Patching Upstream Source

Initially, this question was just for my own enlightenment, but it turns 
out it ties into my ITA on Valknut.

Can changes need to be made to files provided by upstream, e.g. a 
Debian-specific patch or a patch not yet integrated upstream, be done in 
the .diff.gz and be compliant with Standards-Version 3.8.0?  Or, do they 
need to be done as part of the patch target in debian/rules, e.g. via 

I've just come up from my first complete read-through of the debian-policy 
(sans Appendices) and it indicates that it is preferable that such changes 
be in the .diff.gz, so that dpkg-source -x gives a "ready to be further 
patched" source.  However, ISTR advice given on this list that 
the .diff.gz should simply contain the debian directory and then the patch 
target in debian/rules should apply patches from that directory.

It turns out that the valknut package in testing/unstable does make it's 
changes to upstream source in the .diff.gz, and I'd like to update it to 
Standards-Version 3.8.0.  It seems to me to be a little odd not to do the 
patching in a .diff file, but working with something like dpatch would be 
fine -- I'll probably be using git to maintain my work.  Anyway, I wanted 
to double-check what is current policy.  (BTW, if I'm just being thick and 
this is actually clarified in the documentation, just give me a document 
and section and I'll look it up myself.)
Boyd Stephen Smith Jr.                     ,= ,-_-. =. 
bss@iguanasuicide.net                     ((_/)o o(\_))
ICQ: 514984 YM/AIM: DaTwinkDaddy           `-'(. .)`-' 
http://iguanasuicide.net/                      \_/     

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