On 12.10 this still appears to be an issue out of the box.

The biggest problem it causes is that it makes working with one's own
system very frustrating, since you lose the ability to use any GVFS
mounted filesystems between sudo'd nautilus windows (you have to drag to
local machine, then drag to wherever one is working).

There desperately needs to be a configuration option for this.

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https://bugs.launchpad.net/bugs/225361

Title:
  .gvfs can't be stat'd by root causing backup tools to fail

Status in GVFS:
  New
Status in “gvfs” package in Ubuntu:
  Triaged
Status in “gvfs” package in ALT Linux:
  New

Bug description:
  Problem
  =======
  For security reasons ( possible DoS ), other users (esp. root) cannot access 
a fuse filesystem, and not even stat the mountpoint:

      $ sudo stat .gvfs
      stat: cannot stat `.gvfs': Permission denied
      $ sudo ls -la
      ls: cannot access .gvfs: Permission denied
      d?????????   ? ?     ?         ?            ? .gvfs

  This means "rsync --one-file-system" (and similar options for find,
  tar...) cannot know this is a different file system they actually want
  to exclude, and fail on the permission denied error.

  Please note that it is GOOD AND CORRECT that root cannot copy the
  .gvfs directory. The real problem is that the stat fails.

  Workarounds
  ===========
  * bind-mount the file system you want to backup beforehand (see comment #67)

  See also
  =======
  * Excellent description of the problem in bug 227724
  * fuse-devel mailing list saying this will all be solved someday using 
"private namespaces"
  http://thread.gmane.org/gmane.comp.file-systems.fuse.devel/3497/focus=3502
  http://thread.gmane.org/gmane.comp.file-systems.fuse.devel/7169/focus=7236
  http://thread.gmane.org/gmane.comp.file-systems.fuse.devel/6197 (no answer at 
all)
  * Kernel documentation explaing the DoS
  http://www.kernel.org/doc/Documentation/filesystems/fuse.txt

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