I presume you're using ModeShape 3.x. In that case, you've likely configured the repository to store the binary content in that directory.
In that case, ModeShape stores binary values keyed by the SHA-1 hash of the bytes, in a directory structured defined by various parts of the SHA-1 hash (which is nicely distributed). For details, see our documentation.
BTW, that is just the binary value storage. Your indexes and Infinispan storage should be elsewhere; if not, your configuration needs to be corrected. If you have any questions, ask them on our user forums.