You can deploy ModeShape to a server (such as JBoss EAP, Tomcat, etc.) and use the REST API, which would allow your remote clients to upload and download files. However, you might be better off creating your own RESTful web service using simple JAX-RS code or writing a servlet-based application that exposes exactly the functionality you want.
Or, take a look at the S-RAMP governance repository component of Overlord, which is basically a set of web services (on top of ModeShape) for managing and governing artifacts (files) of various kinds. It might actually have out-of-the-box the functionality you want. See their documentation and a few of their blog posts, too.