Hi Joe,
Yes our Learning Objects Repository (LORS) allows you to create or upload via standards (IMS or SCORM) learning object in a hierarchical relationship. When the student accesses these objects they can browse a file/folder hierarchy.
There is a video demo here (looks for LORS-Central)
http://dotlrn.org/demos-dotlrn/
Take a look then feel free to come back with more questions.
Thanks