Annotations for models in subdirectories of engines/subtrees/etc

[djsegal]

I believe this is similar to the following issues: #190, #131, #88

To get it to work on my project, I have the following 2 lines in auto_annotate_models.rake:

 'model_dir'            => ["app/models", "lib/subtree/app/models"],
 'root_dir'             => ["/", "lib/subtree"],

[djsegal]

This has been merged.