Massive renaming and migrations.

* All probe-related projects go under the probe/ directory
  - By sbt binary version, e.g. 0.12/ for current probes
  - sbt binary version included in the name
* Move the remote controller / parent project to top level directory
* Create "commons" directory for sharing raw source code between projects
* Update the build so it succeeds, but all tests still fail.
More cleanups for renaming. Somehow probe had gotten lost.
Shims should now just add any file repository they find.
Fix caching of repositories so we only resolve when needed.
Fix cleanup issue with integration tests.
Fixed integration tests to work again.

* Note to self, don't let `.sbt/repositories` hose us in the future
* Ensure we clean before creating projects.
* Fix shim to include any file based boot repository.
Removing testing code.