Fix warnings and remove some dead code

Begin on rewriting stats and stats output.

Remove dead and commented out code

Add test tet file, and flush out some easy bugs

Greatly simplify the `reduce` method.

Did a lot of things.

This is not tested at all, since CGAL is stupid.

Rework alpha_2d a little, and fix warnings

Move alpha values to `Persistence`

This makes more sense, but it's not optimal still.

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.

Add more cli arguments

Should also do some cleanup with the `Simplex` code.

Move persistence things to new file

We'd like to keep `main.rs` to be argument parsing and stuff like that.

Add a bunch of comments

Move output things to `output.rs`, and fix warnings