The java.library.path can be set before or during the execution of a java app (either by setting the global environment variables of the java library path or by using a flag when running the java exec jar). Can it be set inside the manifest file of the java jar, as is done for classes with Class-Path? Sounds like a feature that should be supported, if it does not exist.
EDIT : since as stdunbar mentioned, the manifest file does not support java.library.path mappings, I've added an answer with an alternative solution to using the manifest file.
No, this isn't supported by the spec. In general, the java.library.path variable would be very O/S and machine dependent and including it in a Jar file would not make much sense.
Since java.library.path can not be set using the manifest file, I looked around for an alternative solution. A nice one is setting java.library.path via the actual application code: setting java.library.path programmatically
This solved my deployment issues like a charm (no need for an additional script to manually set the -Djava.library.path).
Note that if a more dynamic solution is required, the added library path can be stored in a configuration file which is read when setting the java.library.path.
EDIT: Updated link, thanks to @uchuugaka