I am not sure exactly what you are trying to do here, so if I am off a great deal, please forgive me.
If you have 2 different "applications" they are isolated by Tomcat, though a workaround may exist, I am not sure it is needed. You can't really, or I should say shouldn't really run 2 applications from the same folder.
So first of all, what do you mean by link? You can certainly use Java/JSP to query a file in a separate site/application and "include" the output of that directly into your page's output. This is one of the standard include methods available.
The 2 options are 1) to include the target source into your source and run it together, or 2) to query the target source and include its output in your output stream.
If the application is separate, you should really use the second option.
Now, I am guessing here that you mean 1 server with Tomcat and 2 applications...
If you mean 1 application but part running on one server with Tomcat and theother part running on a different server with Tomcat... Then you are looking at distributed computing and/or clustering and that is a much more complex issue...
Where the servers are located in relation to each other, what URL/IP is available for the setup, what sort of distributed architecture do you wish to implement, etc... are all questions that need to be answered first...
IF this is just for development purposes, meaning that they are separate while you develop but will be a singluar system when finished, I say get a CVS (Concurrent Versioning System) of some sort and have you BOTH sync your work regularly with the CVS, then check out each other modules for your dev. testing etc.
I have developers working an several countries around the world at any given time, on the exact same project. Each is assigned specific components to built and maintain during the development cycle of the project. We use an open source CVS which certainly makes us all able to run and test the system at our leasure...
Our system is old and has some drawbacks, I am considering replacing it with a newer variant which I hear is much more user friendly... but even a complex CVS is better than no CVS when working as a dispersed team...
Peace,
