We as a group develop Javascript/JSP web application, and the problem is we are developing the webapps based on customer requests, while another team (core team) develops the "core" webapp product.
In other word, we "customize" the Javascript/JSP webapp differently for different customers, most of the customization is in the Javascript code.
The problem is, everytime the core team releases a new version, we have to merge our customization into the newly released product, and this is quite painful.
In essence, we have to diff our customized webapps against the old version and then diff the old version against the new version, and then sync them up.
What are the best practices to deal with this situation?