Dragos is on the right path. This property should be filled in your Settings.yaml file.
Have a look at the following documentation pages:
A fully documented example yaml file can be found on GitHub: m2ee-tools/examples/full-documented-m2ee.yaml
Search for ApplicationRootUrl
Misc.getApplicationURL() resolves further into Core.getConfiguration().getApplicationRootUrl().
While I'm not sure where you would configure it - perhaps checking the configuration definition in the Java SDK documentation here would help get you on the right path - It's likely that all the properties defined under configuration are set up from the same place.