Refactor the runtime extension repositories to properly support multiple calls to processing assemblies

[mslukebo]

Is your feature request an entirely new concept?
No

Is your feature request related to an existing component?
Yes - the runtime ExtensionRoot and DataExtensionRepository

Is your feature request related to a problem? Please describe.
The PluginsLoader does redundant work finalizing data extensions every time a new set of directories are loaded.

Describe the solution you'd like
The ExtensionRoot and DataExtensionRepository should be refactored to expose an API that natively supports loading sets of directories as plugins at different times.