Which is the trouble with this bug: it's actually several otherwise very minor 
shortcomings that add up to a nasty result.
Apples-to-apples check did fix one problem, but it's circumvented via another.

The second "big" deal, of course, is that usually symlinks are treated as their 
targets, but using this approach in ALL contexts indiscrimiately is bad.
But.
The dialog itself is flawed: it's important enough to show more than a tab 
does, and it shows less.
Icons are good, but why the usual overlaid emblems are NOT applied in 
confirmation dialog? Then symlink would be at least clearly marked as such.
Then, there's "Size:(null)" for directories. Sure, looking inside slows down 
the huge list - but in the dialog there's only one item and for 
merging/overwriting purpose it's kind of important what's inside it, so perhaps 
settings different from the file list (and more verbose by default, at least on 
"X files + Y directories" level, though seeing the size of at least of 
immediately contained files would help too) would improve the situation.

Speaking of dialog, overwriting a directory with file is already unusual
enough that perhaps this should be a separate category for "apply to
all" purpose - just to be on the safe side. Merging a newer directory
into old may call for overwrite of old files, but this shouldn't easily
lead to something so strange and drastic.

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

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

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