clearer description of commit_files args: git_files,annex_files
refactor create,annex_add commands: file lists, no json,xml

Refactor create, entity_create, entity_annex_add so that they
take lists of updated files and of templates to be added.

This is the first step in removing higher-level metadata files
(collection.json, entity.json, ead.xml, mets.xml) from ddr-cmdln.
rm entity_add_(master,mezzanine,access) commands

These had not been implemented and will not never be used because
of the way files are actually being created.  The higher levels
of the stack manage the file role metadata.
rm JSON,XML processing code; rm DDRCollection,DDREntity

JSON and XML metadata files are best handled at higher layers in
the DDR software stack.  This change removes the rest of the code
that deals with JSON and XML, as well as template files.

The DDRCollection and DDREntity classes' only function was to
add metadata to Collection and Entity, so these classes have also
been removed.