When we ingested our data, we did it by the project. So for each project requirements document, we created a module. We have certain requirements that would actually be better off alongside requirements of a similar group, however, they are currently in different modules. Since each module has a content folder, the base artifacts are in a context that isn't ideal. Our goal is to align those base artifacts into the same folders, while also maintaining the hierarchy of said artifacts within a module. In short, our existing modules aren't "modular" in the functionality they express. So in order to make things easier for users (and satisfy the needs of mgmt) we have to reorganize to better fit the pieces of functionality rather than the documents they originally came from. 

Does this make sense? Let me know if you need any additional details. I would really appreciate some guidance on this.