QOL Fixes

[lacraig2]

This PR fixes 2 areas that have bothered me when using penguin.

The first is the calculate_score function which we often see errors out of when repeatedly running Ctrl + C in a rehosting. This PR makes that function much more resilient to issues.

The second is around patch conflicts. Previously, conflicts were written out every time we load our config (at least twice) and they looked like:

13:48:34 config WARNING patch conflict: core.root_shell: `false` → `true`

This information is useful, but it's hard to know exactly what is going on here. Which config patch set it originally? Which overrode it? Why is it printed so much?

This PR makes those more readable and actionable by providing a cleaner name for the config option, the old/new value, and the names of the config patches that held and then were overwritten. In the case that it is in our core config we list it as base_config

15:47:26 config INFO conflict: core_shell: `false` → `true` (base_config -> manual.yaml)

We've also dropped this down from warning to info and updated the settings around it so we only ever see this when we call with verbose=True which we only ever do in penguin_run.