Debugging JavaScript.execute

I am trying to debug the JavaScript component. I am calling the execute method and passing it a Right now I am just using a trivial call like this:

js.execute(“"", "this is foo", "width=400,height=300");”);

Now, the issue I am seeing is that if I do this early in my session, right after I log in, the window comes up fairly quickly. However, on the same page, if I do something to call this later on, the popup takes up to 10 or 15 seconds to come up.

So I want to debug into the execute method, and I have source attached for it, but Eclipse will not let me edit source that is in a jar file.
So, perhaps naively, I pulled the source into my project. Problem is that there were many many code breaks using this method (paths were not where they were expected to be, etc), so I am about to try something different…

My plan is to pull the source to a different project, put in my edits, recompile, and put the jar file back in the locaiton pointed to by ivy.xml.
I am using Vaadin 7, if that makes a difference.

Is there a better way to do this?