gracefully skip over files with unparseable syntax

also got rid of File and Source entities and simplified Root entity

Change-Id: I44721201e0576e20bf59dfa6d0a16fc4a436683b
Reviewed-on: https://gerrit.instructure.com/46378
Reviewed-by: Coraline Ehmke <coraline@instructure.com>
Product-Review: Michael Ziwisky <mziwisky@instructure.com>
QA-Review: Michael Ziwisky <mziwisky@instructure.com>
Tested-by: Michael Ziwisky <mziwisky@instructure.com>