Complete Makefile from the root is actionable, closes #18.

- Added Python and Vim stuff to .gitignore
- Developed a complete Makefile in the root directory.
- Moved the outline into its own file.
- Created build instructions and moved into the root README.
- Added a default config file.
- Regenerated the figures and tables.
- Removed the old config file.
- Added print statements to python scripts and did some cleanup.
- Created a function to load the paths in the config file.
- Added Octave link to README.