This use case is important!
When synchronizing two folders in subversion (same issue with CVS) I use file filter to ignore .svn folders. However, when I'm copying new subfolders, their .svn subfolders get copied also. And this leads to quite a mess sometimes.
So I think we should optionally apply file filters also when copying and only copy "visible" content, not folder's real content.
This has been discussed in developer forum also:
Folder compare improvements and ideas?
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