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I've upgraded from Ubuntu 12.10 that I installed with Wubi, to Ubuntu 13.04.

When copying a folder from my secondary hard drive to a folder located in "/host/" with the same name, "Files" asks me if I want to merge these two folders. After clicking "Merge", it overwrites existing files that have the same name instead of asking me if I want to skip replacing them.

In 12.10, Nautilus 3.4.2 asked me if I want to skip overwriting existing files. Now, in Ubuntu 13.04 with Files 3.6.3, it overwrites files without asking me, but only when I merge a folder with one located in "/host". Maybe it's a bug in this new file manager.

What can I do?

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Nautilus was given an over haul so it conforms to "Tablet" mentality. They also removed the split screen feature as well (F3).

So in short, you can't unless you install another filemanager

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