You can just contribute in the project. We currently have nearly no resources for development. We can support development though. The most important thing is a clean architecture. I would propose Angular2 for UI and JAX-RS for backend development. In other words: http://www.dropwizard.io/ plus Angular2.
If it is OK, I will invite you to our slack channel. Maybe other volunteers join there, too. Then, we can have a chat there.
Currently, JabRef has imports for various formats and no direct command line for it. Why not using JabRef as library where you can directly create a bibentry using plain Java methods?
I would "just" include JabRef in a JAX-RS environment and expect the UI to post bibtex as JSON.