Added a helper method that creates a new uri by adding an index, version identifier, or other id modifiers to an existing uri.  This is expected to be useful for implementing copy methods for SBOL objects.  A copy method for DNAComponents was implemented.
Implemented procedures for deep-copying SBOL objects and minting new uris for them.  The augmentURI method is useful for modifying uris to keep track of different instances and/or versions of objects.  (The SWIG Python interface was updated to export the new copy methods.)
Revised documentation
Made several changes concurrently.  In progress are modifications to both reader and writer to allow structured annotations to pass through.  This is an advance feature of libSBOLc version 2.0.  An array of structured annotations was added to the base SBOL object.  Presently, the reader can locate annotations in an sbol.xml file by namespaces not matching known SBOL namespaces.  It then outputs the contents of these extra annotations as raw text. Documentation was updated and pushed online.
Most recent changes to serialization were temporarily stashed by commenting out the relevant lines of code.