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
I don't believe these new attributes are present/documented in `sentence.py` or `document.py`, are they? `sentence.text` might be especially confusing, since `sentence.sentence` is used everywhere else in the code.