APE3: Config system improvements

WIP.

This currently implements the "changes to the base configuration system" part of the APE.

Hit a bit of a road block, since it's not possible to update configuration values in the default configuration file, since they are commented out by default.  We first need to find and remove the commented out value to replace it with a real one.  ConfigObj doesn't really handle that directly, and not sure how to handle it in the general case.