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When I mount a samba network share in nautilus it is mounted under ~/.gvfs I would like to change this default so that all network shares mounted using nautilus are mounted under /mnt for example.

How would I go about doing this?

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As far as I can tell, there isn't a way. You can link ~/.gvfs to your home folder(~/shares or /mnt even) if you wanted.

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When running compilation scripts with cmake within these linked folders, the symlink isn't respected and the original mangled path is used, which breaks cmake. Mounting is a solution but mounting requires root access. The allow_root option is mysteriously ignored. Strongly considering dropping support for gvfs – Nuzzolilo Jan 1 at 10:30

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