To simplify the project and make it easier for people new to the project I suggest the following new folders structure. This is based off of other similar projects.
/ - The root directory will have the Make file for the application and a README.md file with instructions for how to install and launch the application. It will also have any files that don't clearly belong to one of the sections below.
/server - This folder will contain back-end code that will run on the BBB to establish an HTTP Server that will enable communication with a browser running on the Client computer/device.
/client - This folder will contain the front-end HTML, CSS and Javasript code that makes up the Client side App.
/robot or robocupjr - This is the folder that will contain the code used to control and manage the robot systems like OpenCV and Motor control.
There will also be subfolders within each of these directories that will break down the sections, but only as much as is necessary to help with understanding how the project fits together and in finding things quickly.
Examples: * Client Folder Structure