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Normally, within a directory, only one document can exist with a particular document name. Attempting to upload a document with the same name as an existing document in the same directory node will generate a warning message and the user will be invited to choose, either to overwrite the existing file, or to create a revision directory and save a new revision of the document.
Within a Revision Directory, documents with the same name can co-exist. This functionality enables users (with appropriate access privileges) to upload a new revision of a document without overwriting previous versions. Users, can elect to download the current (default), or an earlier version of a document. The document revision that you intend as the 'default' can be changed by anyone with the appropriate access privileges (see revision directory properties).
If nodes were linked/embedded/attached to a document before the document became a revision then whichever is the 'default' revision of the file will be associated with the node