When uploading, there is no way to disable hidden files from being uploaded. So, all the nested .svn folders get uploaded with the files. For CVS, they aren't hidden, however it would be good if there was a way to tell it not to upload these directories also.
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A way to exclude files from being uploaded is described in http://cyberduck.ch/help/en/faq/index.html (see the bottom of the page). I take this as a user interface request to make this option available in the preferences of Cyberduck.