STK is a module, it's not a web app. You need to build a web app that you deploy in Tomcat. To build a web app (with maven) you can just overlay magnolia-empty-webapp and add dependency to STK or you can simply overlay magnolia-bundled-webapp that includes STK (among other modules).
However consider also this: To extend STK you don't need to change it directly, you can just create your own module with dependency on STK and reconfigure default implementations of models or whatever else you need to change with your own impl of same interfaces. This way you can easily upgrade to newer versions of STK while keeping your changes safely separated.
You might also want to read this post about building projects based on Magnolia.
HTH, Jan