Note: This is an optional migration step
Unless you are running two different stores that share web services and not any presentation layer components, you will find it easier to deal with only three Maven modules instead of five. This is actually a pretty easy migration to do.
The first step is to physically move some files around to fit the three module structure. You will basically want to move all files in admin-war into admin, maintaining the exact same folder structure the files are already in. The same applies for site and site-war.
In the parent pom.xml, you will want to remove the admin-war and site-war module defintions and any references to these modules. You will also need to add any dependencies that were in admin-war into the admin pom.xml, and again, the same applies for site.
You will need to update references in your project to the new file locations. This will depend on your application, but will likely include changing references to files inside JARs like this:
to ones that reference files directly in the WAR like this:
You can see an example of what was involved in collapsing the modules on this GitHub commit