Should we bundle configuration files along with Jars?

In Appzillon IDE,by default Bundle Web/Server Properties (Build Server > Preferences > Bundle Server Properties, Build > Web > Bundle Web Properties) are checked.
I would like to know which approach is better
1. Bundling configuration files like Log4j, Camel-context, appzillon-server-commons etc along with jars.
2. Unbundle configuration files and place it in separate folder under WEB-INF/lib.
It depends on your deployment cycle, if your application undergoes frequent changes to the Web/Server preferences then externalised properties will server you the best.

Unbundled properties files should be placed within server's class path and need not be always with in WEB-INF/lib folder.