newby question about merge.

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Hello I am using git to deal with debian packages.
So i have two Branches the "upstream" one with the different version of
the programm I am packaging.

exemple with two tags

scigraphica/2.1.0
scigraphica/0.8.0

I have another branch the master one which is the upstream + the debian
directory.

So I do a merge like this
"git merge upstream ." when I am on the master branch to work on the new
package.

Everything is fine until git merge the configure scripts. (autotools)
there is conflict with the configure file of the 0.8.0 version during
the last merge.

My question is how can I keep the upstream version of the configure
file instread of the one in the working directory.

I read about the stage(1:2:3) but I do not know how if it is related to
my problem.

Thanks in advance.

Frédéric
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