Currently SetFeatureCompatibilityVersionCommand::run and _runDowngrade can be confusing to read and understand where to place any necessary uasserts. We should investigate whether we can refactor _runDowngrade and create new helper functions with comments explaining what the new organizational structure is . For example, one helper function could be where all the user collections clean up uasserts go, another one could be where all the internal server cleanup should go. We should also investigate whether we can have helper functions based on the role/phase of the node (config server vs shard server vs single replica set/standalone).

As part of this we should also audit old branches for what types of things could be done on upgrade/downgrade.