Hello Benoit,
I gather you are trying to build a single fat jar that contains all of your code and the Trooper binaries. Is that true? That unfortunately is not possible - you need independent jar files at least for Trooper modules.
The configuration files under /resources/external are meant to be deployed outside the application jar. These are picked up by Trooper using the FileLocator class (this looks into config locations i.e. /resources/external and on the classpath). The only deviation to this is bootstrap.xml which is specified as absolute path since it is the startup configuration.
You may deploy as follows:
a) Package all binaries into module specific jar files (say via maven build) - for e.g. you will have jars like batch-core-1.2.3.jar, your-app-1.0.0.jar etc.
b) Deploy the config files i.e. XML files into a directory that follows /resources/external anywhere under the projects root specified in bootstrap.xml
Here is a Maven build file that deploys Trooper batch (copies dependencies to enable execution from command line) :
You can then run your Trooper like this:
java -cp ".target/your-app-1.0.0.jar:./target/lib/*" org.trpr.platform.runtime.impl.bootstrap.BootstrapLauncher ./src/test/resources/external/bootstrap.xml