Improve performance of parse_yaml?

[anne17]

In parse_yaml, when only some resource types are being updated, it is probably unnecessary to re-write the JSON files for all resource types.

However, resource collections and file deletions still need to be handled correctly. I.e. when a collection YAML file was updated, the JSON file belonging to the resource type of that collections needs to be updated as well. And when a resource file was deleted the JSON file belonging to that file's resource type needs to be updated.