Remove need for repo.bootstrap.modules for auto-export

The auto-export module configuration contains a mapping from maven module path to repo paths for processing auto-export diffs. We should use this info to determine which modules should be loaded from the filesystem as source, rather than requiring a separate system property for this purpose. This will require careful ordering of bootstrap processing (and possibly a partial repeat of module loading) to avoid using stale auto-export config.

AKA HCM-154