Infractructure cleanup

• Infrastructure: I reimplemented most of the main functionality with cleaner code, having learned from many lessons and surprises from initial development.
• Robustness: I am using safer mechanisms to search for dependencies and map out user-side workflows so that drake is less likely to fail on edge cases.
• Documentation: I refactored the vignettes, and I baked an example of a common use case into the code.
• High-performance computing: distributed computing with Makefiles requires expensive overhead, so I added a low-overhead single-node alternative (using parallel::mclapply()).