Extend the Config System to allow users to control how configurations are stored

[mmetcalfe]

The Config System currently stores configurations on disk in a single colossal file.
This means that saving the current configuration to disk takes a long time - no matter how few parameters have actually changed.

A planned extension to the Config System is to allow users to choose entire branches of the tree that should be stored in their own file.

This would allow faster saving (and potentially, loading) of configurations when only a small number of parameters in the tree have changed - which could be useful for e.g. machine learning applications.