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
To me, it seems there were two advantages to having this code like this: first, an error with one file wouldn't stop the entire processing pipeline, and second, it was easy to see which files were causing errors.