Restructure Code, Data, and Paper tags

[infispiel]

Previously, MEDFORD was defined to use data-type & etc to declare whether it was a reference, copy, or primary. This has since been changed. All Code, Data, or Paper lines with URIs should be changed to Code_Ref, Data_Ref, and Paper_Ref as appropriate. All lines that refer to a specific file without a URI should be changed to Code_Copy, Data_Copy, and Paper_Copy as appropriate, with a copy of said file placed into that medford file's subdirectory.

(Also, the Software tag should be updated to Code in all instances.)