We have a cloud based CTI Integration client Website.  The website team provided a vendor code and asked to deploy in pega in the prweb context. How to combine the vendor code with prweb war on the websphere server, so that all the code is available for communicating with call client website with two browsers working sessions in the same user desktop with java script code.

does not feel like the right approach. prweb.war has bare minimum bootstrapping code and should not be manipulated.I think you need to use Pega built-in Rule-HTML, etc to incorporate your client code. There are a lot of examples within the platform with html/js all stored in Pega database. If you can specify more details of your code, we may be able to experiment with more certainty.