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
Moved and renamed reader_writer.py
Fixed one exception during testing by creating an autospecced mock in unit test.
Unit tests now pass, some lines will have to change after integration.
Merge branch 'keien'