Adapting to changes in runtime configuration

[julianharty]

Context

Our main scripts are long-running and designed to continue processing from where they previously finished. What they don't currently account for are any changes to the runtime settings e.g. if previous runs didn't keep local copies of a repo and the current run does, should it backfill our local cache of repos that were analysed previously? And if so, what should it do if the most recent commit has changed since the previous analysis?

For the moment, this ticket is to track the current behaviour and the effects. No code is needed at this stage. TBD once we've made more progress with the rest of the work.