Redundant files and organization

[iamciera]

The code folder is a little crazy. attn: @alexnakagawa, @jshi1010

Few issues:

1. What is the difference between these two files?
   motif_mapping.ipynb & Motif_Scoring_and_Extraction.ipynb. Is the motif_mapping file just for D3 building?

2. Motif_Scoring_and_Extraction.ipynb filename should be lowercase: motif_scoring_and_extraction.ipynb

3. We should split the command line code (map_motif.py) from the Jupyter notebook code and maybe even the an additional folder for D3 code. The structure could be py, ipynb, and D3. Thoughts?