I have been working on a project that is hosted of site. I am worried about putting the bridge server in the root folder with all the info it holds.
The way you ask your question seems to imply you think of the bridge server as working like a PHP application where you drop files in a folder and then immediately the app becomes available to the world.
The bridge server is meant to be run as a standalone process and exposed only through an HTTP port. It does not publish the files within its installation directory through the HTTP endpoint.
To host a bridge server, simply configure it and run it on a server. You'll need full access to the server host, not just access to drop files like most of the cheaper web hosts provide.