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.