With automatic indexing turned on, the folders and files you upload are assigned a sequential number that corresponds to their upload queue.
Later, if necessary you can move the files and folders around within the structure by either renaming them from the context menu or drag-and-dropping to the necessary position in the structure.
To eliminate gaps after deleting or moving documents, use the "Rebuild index" option to regain sequential numbering.
Rebuilding index works folder by folder as well as for the parent folder, i.e. entire VDR structure.
Please keep in mind that the folders are always placed above the files in the structure.