Add apply(String) and apply(Class) to PluginAware.

+review REVIEW-5298
Don't deprecate any of PluginContainer.

+review REVIEW-5298
Add note to backlog for supporting an environmental version of `--parallel-threads=N`
Remove AppliedPlugins and make PluginManager the public replacement for PluginContainer.

+review REVIEW-5298
Change the tangling between DefaultPluginContainer and DefaultPluginManager.

+review REVIEW-5298