Reorganization

Reorganized the program.

- Pipeline is now in `app/pipeline`
- Removed `lib/`
- `install.sh` and `config.py` have been updated for new location of stanford library.
- Moved pipeline files that were alone in their directories up a directory
- Moved together all documentation, fixed incorrect docstrings and missing links (documentation compiles without errors).

Closes #77, closes #68.