Yes, it is possible to 'merge' the contents.
For this, you need to load an application.properties file in the external path while using -jar option.
The key was PropertiesLauncher.
To use PropertiesLauncher, the pom.xml file must be changed like this:
<configuration> <!-- added -->
<layout>ZIP</layout> <!-- to use PropertiesLaunchar -->
After the jar file had been built, you could see that the PropertiesLauncher is used by inspecting Main-Class property in META-INF/MANIFEST.MF in the jar.
Now, you can run the jar as follows:
java -Dloader.path=file:///C:/My/External/Dir,MyApp-0.0.1-SNAPSHOT.jar -jar MyApp-0.0.1-SNAPSHOT.jar
Note that the application jar file is included in loader.path.
Now an application.properties file in C:\My\External\Dir\config is loaded.
As a bonus, any file (for example, static html file) in that directory can also be accessed by the jar since it's in the loader path.