Isolate Aether in a separate class loader

Prior to this commit, the Aether-based GrapeEngine was loaded in the
same class loader as the rest of Boot. This led to Aether's and its
dependencies' types polluting the application's class path. Most
notably, this caused problems with logging as the logging framework
could be permaturely initialized.

This commit isolates AetherGrapeEngine, Aether and its dependencies
into a separate class loader. This is done by customizing the
packaging of the CLI's jar file with the internal directory housing
all of the types that will be loaded by the separate class loader.