indicate dependencies' Python3 support in requirements.txt
mv collections list func -> DDR.models; ead.xml -> collection.json

Moved collections list function into DDR.models because it's
analogous to the entities and files list functions.

When looking at directory, a collection.json file marks it as a
collection.  We may not always have ead.xml files.
sort collections/entities/files list in natural order (not ASCII)