Sorry to be so direct: No, you should not combine hierarchy and pagination in this way. Both are difficult to use by themselves (although they are ubiqitious).
Why do we use pagination instead of scrolling: This is an implementation hack, invented for web pages, to reduce the traffic required to load the page, and thus speed up time to first interaction. Pagination does not originate in the user's mental model, it's a technical workaround for a technical problem (limited bandwidth).
Directory hierarchies are a technical construct as well. Although they are also called "folders", they are drastically different from folders, which in reality can never be recursive (folders containing folders containing folders... you get it). It is an easy way to organize the data bytes in this way, but it places the burden of organization and recall on the user.
If you want to stick to these technical workaround, use breadcrumbs to represent the directory hierarchy, and pagination to represent the list of files in the current directory, separately.
If you want to serve your users better, get rid of the directory hierarchy altogether, and use a tagging system and a powerful search (in line with Mike M's answer). Tagging a document, instead of filing the document in a specific folder, has the added advantage that several tags can be assigned to the document, while a document can only be saved in one folder. Then, make the file/folder structure invisible to the user.
You might want to read Alan Cooper's "About Face 3" for more about implementation models vs. mental models, and the file/folder structure shortcomings.