From mboxrd@z Thu Jan  1 00:00:00 1970
From: Elijah Newren <newren@gmail.com>
Subject: Re: Filter certain files on rebase
Date: Sun, 26 Sep 2010 19:51:12 -0600
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References: <20100921080049.GB27575@nibiru.local>
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On Tue, Sep 21, 2010 at 2:00 AM, Enrico Weigelt <weigelt@metux.de> wrote:
> Hi folks,
>
>
> is it somehow possible to filter out certain files on rebase
> operations. The problem is: I'm maintaining a lot of downstream
> branches, where sometimes upstream leaves in autogenerated files
> (eg. configure) which I want to get rid of. When I just remove
> them by another commit, I'll get conflicts on next rebase.

Use a custom merge driver;
http://stackoverflow.com/questions/928646/how-do-i-tell-git-to-always-select-my-local-version-for-conflicted-merges-on-a-sp/930495#930495
has a pretty detailed example.