Add support for subdirectories in classdir when using schema-tool --create

Currently when using schema-tool --create, all entity classes have to be in one directory. Subdirectories are not supported and result in errors. The iterator tries to require the subdirectories. This makes it impossible to use schema-tool --create to create the database for models that use namespaces and follow Doctrine rules for placing the files in subdirectories.

The schema-tool should iterate through all of the subdirectories of the classdir to find all of the entity classes. It should also not try to require() any directories.