Preparation: You can use step filters as described here. Then whenever you step-debug through your code, it will not jump into excluded packages or classes, e.g. from the JDK or some frameworks like Hibernate or Spring. But this is just a prerequisite.
Solution: The stacktrace still contains frames from those those packages. In order to filter out those as well, you need to patch the Eclipse JDT Debug UI plugin. Someone else has done that already for older Eclipse releases up to Indigo. Because I was curious if I could get it running in the current release Luna 4.4.1 as well, I recreated the other guy’s changes and pushed the Debug View + Stack Filter Plug-In to GitHub including a download link to the patched plugin. So if you are also on 4.4.1, you are lucky and do not need to patch and compile anything by yourself. Just use my version. Otherwise please clone my repo and look at the changes, then apply them to the plugin version of your choice.