Added reader_writer.py and __init__.py and made minor changes to the following:

collectionprocessor.py:
- removed try catch block for easier testing

logger.py:
- added _model_changes to comply with flask-sqlalchemy

documentparser.py:
- changed document.sentences to document.all_sentences to match the model
- changed sentence.sentence to sentence.text

sequenceprocessor.py:
- removed comments from index_sequences
The reader writer has always used the models from the application; otherwise it wouldn't actually do what it's supposed to do.

I'm fine with leaving this off until you get back so we can work out the issue while we merge in the pipeline.