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I am surprised I couldn't find this in the queue, and hope I'm not missing something obvious.
I want to use IMCE for basic file management, allowing other users to upload new versions of their Word documents, etc. Of course, there are links throughout our site to these documents, so new uploads should keep the existing name. I don't want anything done in error, so I would like to rename existing (or otherwise ask the user if they want to really replace existing). I know this is lacking in core as well (see http://drupal.org/project/upload_replace, which doesn't seem to help IMCE any).
So at a minimum, I'd love to see one more option ("Rename the existing file.")under "Default behaviour for existing files during file uploads:". In an ideal world, also allow the user to specify at the time of upload.