refactor phony layer transform to handle all phonies equivalently, including annotations
adjust priority order for annotations
add an optional tei:idno to annotation documents
first pass at annotation support in combine transform, old tests pass, new tests not yet added
allow a file to have no dependencies
convert all remaining xml:id to jf:id in the resolve stage
annotation docs are transformable
basic annotations and tests
annotations for parallel documents
handle annotations with broken up hierarchies
Merge branch 'feature/annotation-support' into develop

Closes #126, closes #127 and closes #128