I'd like to create a simple command line script that will copy some files from ~/myfiles to files on a WebDAV-mounted filesystem over a network connection. I can easily click on places and bookmarks, enter the password/username combo and it'll mount from within Nautilus, but I can't find the location of the filesystem anywhere with the mount command so I can't very well do anything non-GUI to manipulate files.

Will I have to find a way to manually mount the share to a mount point, or is there a way to get it to show up in Nautilus and the filesystem at the same time?

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Afaik, shares mounted via the 'Connect to Server' tool in Nautilus end up under ~/.gvfs. However, there were some issues navigating webdav shares mounted via this tool, see this bug report.

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You want to try FuseDav:

sudo apt-get install fusedav

Then follow these instructions:

http://manpages.ubuntu.com/manpages/hardy/man1/fusedav.1.html

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