Break out core evaluation into its own function

[jeremykubica]

This is step 2 in enabling runs on individual trajectories and largely parallel of step 1 (#445). Breaks the core evaluation of an individual Trajectory into its own function.

Surprisingly timing using the diff test show this runs faster than the monolithic version.

Also deletes a function that has been commented out.

[jeremykubica]

Step 2 of N in #447