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    <p>I've never used the <code>subtree</code> strategy, so maybe this is a suboptimal solution (and maybe it won't work ^^), but you could apply all the new commits in <code>upstream_lib</code> to a temporary branch off of the <code>master</code> line and then merge that. What I have in mind doesn't fundamentally fix your situation, so you'll have to do this kind of "manual merge" every time you want to pull in new changes, but here's how it works:</p> <ol> <li>Determine the fake common ancestor in the <code>master</code> ancestry line, say <code>master~100</code>.</li> <li>Determine the fake common ancestor in the <code>upstream_lib</code> line, say <code>upstream_lib~150</code>.</li> <li>Make a throwaway copy of the <code>upstream_lib</code> branch: <code>git branch --no-track new_upstream_lib upstream_lib</code></li> <li><p>Rebase <code>new_upstream_lib</code> onto <code>master~100</code> using the recursive strategy with the subtree option. (I don't think you can just use the subtree strategy because, as you say, the <code>lib</code> directory in <code>master</code> has changes of its own.) Here's a completely untested command for this:</p> <pre><code>git rebase -s recursive -X subtree=lib --onto master~100 upstream_lib~150 new_upstream_lib </code></pre> <p>Note that <code>new_upstream_lib</code> now has the whole <code>master</code> tree in it, even though you only care about the <code>lib</code> directory.</p></li> <li>Merge it: <code>git checkout master &amp;&amp; git merge new_upstream_lib &amp;&amp; git branch -d new_upstream_lib</code>.</li> </ol>
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    1. POHow to force a common ancestor in a git merge?
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    1. USJo Liss
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    1. POHow to force a common ancestor in a git merge?
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    1. COIt worked perfectly, thanks!
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    2. COI guess the only problem is that there's no shared history or commits with the upstream_lib branch, but I can live with that.
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    3. COGlad to hear that! If you wanted to force the shared ancestry, you could create an initial empty commit and rebase both `master` and `upstream_lib` onto that. Assuming of course that `upstream_lib` is your own branch rather than a remote. However, if the initial import of `upstream_lib` into the `lib` directory was only a `cp` rather than a merge (as described at http://www.kernel.org/pub/software/scm/git/docs/howto/using-merge-subtree.html ), you'll still have the problems you describe.
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