This week's book giveaway is in the OCAJP 8 forum. We're giving away four copies of OCA Java SE 8 Programmer I Study Guide and have Edward Finegan & Robert Liguori on-line! See this thread for details.
You can execute a native command with either java.lang.Runtime or java.lang.ProcessBuilder. You would do well to study the pitfalls of these commands. You should also be aware that JSP's are intended for presentation logic, not what we call "business" or application logic. It is a Best Practice to separate your logic and presentation layers.
The 3rd link in a Google search for "Java" and "cvs" shows jCVS, which may meet your requirements. Since they even have Servlets that provide much of your desired functionality built already, you may just have to work on some of your presentation layers.