clean up extraneous files and organize a bit more

[jbloom]

Remove the Untitled.ipynb and gitignore.txt file from the repo, and move scratch notebooks that are not part of the pipeline (like your color_pdb_functionaeffects.ipynb notebook) to a subdirectory called scratch_notebooks that has a README that explains these are manually run notebooks outside the pipeline.

[arjunaditham]

I removed extraneous files and notebooks. I created a 'scratch_notebook' directory with a small README.md to explain the uses of each notebook. untiltled.ipynb and gitignore.txt were deleted as extraneous documents. Please reopen if dissatisfied.