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Ive installed ubuntu-32bit on windows7-32bit with wubi. Before that I had only ubuntu on my hard disk. It seems like my "home"-folder is the same as my windows home folder. Do I put config files in there? It seems like the directory structure is different than I had before when I only had ubuntu OS on my hard disk. Thanks for advice!

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I don't fully understand your question, so I'm afraid my answer will include a bit of irrelevant information.

When you use Wubu, Ubuntu resides in a disk image, which lives as a single file on your Windows partition (c:\ubuntu\disks\root.disk). Your Ubuntu home folder is there too. This, by the way, makes all disk access much slower when you've booted Ubuntu through Wubi, compared to a native installation, or at least that's my impression.

When you've actually booted into Ubuntu, you can access the Windows filesystem at /host, which is the only directory structure difference that I can think of. (When you use a regular Ubuntu installation alongside Windows, in a dual-boot configuration, the Windows filesystem is usually at /media/disk or something similar.)

I haven't played with a Wubi system in a long while, but I find it easy to believe that Wubi creates a symbolic link (or a few) from your Ubuntu home directory to your Windows home folder. I don't think the entire home directory will be shared -- Ubuntu and Windows use different filesystems that support different features, have different filename restrictions, etc -- but I suppose the Desktop folder might be.

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