As part of #3126, we want to make vg index understand what indexes are needed for Giraffe and the other tools, and how to make them, and have it have a bit of smarts with regard to what indexes can be made and which jobs can be run in parallel. We also want to push down some of the things we learned about "good" pruning and path covering from toil-vg and/or our custom scripts into vg itself.

I made #3142 based on the existing IndexManager, but it turns out that Jordan has been working on a much cooler implementation that's more of a data-driven planner, which will be easier to extend with new rules and the ability to think about resource constraints.

This issue tracks implementing this new planner-based index management system, using it to replace IndexManager, and plugging it into at least some of vg index.