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[TBeholder <95854@xxxxxxxxxxxxxxxxxx>]

Ran into this one too, in a different way.
What makes it even worse: if you merge directories, it's MUCH more likely than usual that at least one of them contains symlinks into another. And then moved symlinks overwrite their own destinations. With files you at least retain something useful...
I just tested it meging two ".../test/" - destination contained a real non-empty subdirectory and source contained symlink to it with the same name. Oh, yes, nautilus does ask whether to overwrite. The problem: it asks this -

File conflict
Merge folder "1"?
Another folder of the same name exists in "test"
...

["folder" icon] Original file
Size:(null)
Last modified: 11:22

["folder" icon] Replace with:
Size:(null)
Last modified: 11:33

Which gives an impression that they are of the same type and both are
empty - while neither is true. Thus the user trusting the dialog is
going to confirm, and have the real directory overwritten with now-
broken link.

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https://bugs.launchpad.net/bugs/95854

Title:
  Folder is overwritten with a file with the same name

Status in Nautilus:
  Confirmed
Status in “nautilus” package in Ubuntu:
  Triaged

Bug description:
  Binary package hint: nautilus

  SUMMARY

  If you copy a file with the same name ("Photos", no extension) to a
  folder which contains a folder ("~") with the same name ("Photos"),
  the folder "Photos" will be overwritten completely

  This is how I lost all my photos  (guys, DO backup!)

  ProblemType: Bug
  Architecture: i386
  Date: Sun Mar 25 11:49:14 2007
  DistroRelease: Ubuntu 7.04
  Uname: Linux acer 2.6.20-12-generic #2 SMP Wed Mar 21 20:55:46 UTC 2007 i686 GNU/Linux

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