Move code to top level

Fix Makefile, add comments, and break persistence.rs

Have started factoring out the `r_when_born` from `Simplex`, since
this shouldn't be there. The only thing the `persistence` module
should need to know of the simplices are their boundaries.

Should consider moving the alpha thing out, or to another module.

Push table in pdf to bottom

Add percent difference in tables

Slightly improve plots

Add perf stats in listings.pdf

Remove dead code, and write perf stats to file

Generate a document with all images and plots for datasets