[STORY] Add option to stage command to specify the format of associated files

[tclose]

Add a --file-format <mime-like> option to the stage command to register file-formats that should be matched against associated files. These formats will be iterated through to see whether the detected files match this format.

Another option --from-metadata <mime-like> (id|resource) <header-key> should be added that allows the ID and resource of a scan to be read from the metadata of an associated file instead from the path