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    <p>No, this is not the expected behaviour. The reason it was leaving all the changes as modified files was because it had "given up" on the merge.</p> <p>Information that I did not know was relevant at the time of the posting -> I had created the repository originally not knowing about putting .DS_Store in the .gitignore file. I have had *.DS_Store there for a long time, but I probably hadn't cleaned up properly after doing that. It looks like there were "many" .DS_Store files in the repository and putting it in the .gitignore file appears to just mean "from now forward", not "from what I did before".</p> <p>So above, Xcode complained about the .DS_Store file being modified and since it didn't know how to resolve conflicts in files of that type, it just gives up. It didn't handle the fact that the file had been deleted already in RepoA, it needed to be deleted in RepoB too. Secondarily, although it said .DS_Store in the file list, it was not the .DS_Store in the main folder, it was one or more .DS_Store files somewhere down the file hierarchy. So no matter how many times I deleted the top level .DS_Store in git via the command line, Xcode was never happy. So I couldn't tell <em>which</em> .DS_Store file it was talking about. Looks like Xcode is not good about having multiple files of the same name in your project.</p> <p>Fix is to follow another <a href="https://stackoverflow.com/questions/107701/how-can-i-remove-ds-store-files-from-a-git-repository">SO post</a> where you find all the .DS_Store's in your hierarchy, git rm them and then git commit all via the command line. Then the Xcode merge will complete and you won't be left with modified files from a pull.</p>
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