The file-1 label should be matched by:

   ((?P<classname>%s)(?P<id>[-\d]+))?  # optional leading designator

if you have a class called "file". In the classic schema the file
class is define by:

file = FileClass(db, "file",
                name=String())

If you rename "file" things will break.

It is quite possible there is an issue here, but please
verify that you have the proper classes defined.

You have pointed out that @note and @file are coupled to specific
elements of the schema and that is not pointed out anywhere that I
can see in the docs. So that should be fixed.