Calibre is not just indexing. It's also modifying data.
Of course, if Calibre would have source book concept, it could treat arbitrary directory as sources and map converted and massaged documents and metadata to them.
You can export files into customizable directory structure.
If you want to arrange files to directories, you can export documents into arbitary directory structure determined by big number of attributes and even tags.
Of course, if Calibre would have source book concept, it could treat arbitrary directory as sources and map converted and massaged documents and metadata to them.