Completeness test

Here is what I am adding to/changing in the pipeline:

- Reorganized and changed imaging_pipeline.py to cover the new png files.
- Added a test to se if make_output_dict in imaging_pipeline.py is correctly working.
- Created a script setup_logging.py to do the set up for logging.
- Created a script check_filesystem_compleness.py to look for missing files.
- Created the settings.yaml and the template for it.
- Reorganized the file tree.

Ok this needs to be changed, this is my fault. If you look closely you can see that I've hard coded the module name to be `check_file_completeness`, which makes no sense for a general utility. It should look like this instead: 

```python
def setup_logging(module_name):
    """Set up the logging for the mtpipeline scripts.

	Parameters:
		module_name : string
            
    Returns:
        nothing
            
    Output:
        nothing
    """
    log_file = (module + '_' + 
    			datetime.datetime.now().strftime('%Y-%m-%d-%H-%M') + 
    			'.log')
    log_file = os.path.join(SETTINGS['logging_path'], module, log_file)
    logging.basicConfig(filename = log_file,
                        format = '%(asctime)s %(levelname)s: %(message)s',
                        datefmt = '%m/%d/%Y %H:%M:%S %p',
                        level = logging.INFO)
```

Notice the changes I made in the docstrings and see if you have any questions.