Making an executable JAR with Maven

I'm using Maven for my project and it works great for running my application. However, when I deploy the application to a JAR file, it flattens the natives directory and thus JOGL cannot load the native libraries because the naming scheme is incorrect.

What do I need to do to make Maven include a natives/ directory?

This is what I currently use in my pom.xml:

                        <plugin>
                                <artifactId>maven-assembly-plugin</artifactId>
                                <version>2.4</version>
                                <configuration>
                                        <archive>
                                                <manifest>
                                                        <addClasspath>true</addClasspath>
                                                        <mainClass>path.to.MainClass</mainClass>
                                                </manifest>
                                        </archive>
                                        <descriptorRefs>
                                                <descriptorRef>jar-with-dependencies</descriptorRef>
                                        </descriptorRefs>
                                </configuration>
                                <executions>
                                        <execution>
                                                <id>make-assembly</id>
                                                <phase>package</phase>
                                                <goals>
                                                        <goal>single</goal>
                                                </goals>
                                        </execution>
                                </executions>
                        </plugin>

Hi

Maybe you can call an Ant script within Maven to fix that. Why not using maven-nativedependencies-plugin?

I'd rather not have to make an Ant script to fix the Maven build! How would I use maven-nativedependencies-plugin for this?

Please look at the example project here and you can adapt it to use JOGL:
http://code.google.com/p/mavennatives/

I'm not sure it does exactly what you want. Maven is very rigid but based on Ant, using Ant with Maven isn't weird (with antrun-plugin).

I have found no way of using a file mapper or disabling the flattening, it hasn't been implemented in Maven:
http://jira.codehaus.org/browse/MASSEMBLY-45

Edit.: Have you tried to use dependencySet?
http://maven.apache.org/plugins/maven-assembly-plugin/assembly.html

I never liked the fat-JAR approach (sooo many problems) so I distribute a ZIP-file. But I guess that the same tricks I use can be used to make a fat jar without flattening.

This is one of my assembly.xml : https://code.google.com/p/svansprogram/source/browse/application/svansprogram-assembly/assembly.xml
This takes all project dependecies and put in a "lib" directory (the first dependecySet), I set unpack=false because i don't want the JARs unpacked. Then I take the executable JAR and put in the directory above the lib-directory.

However, what you could probably do is use several dependecySets, but with unpack=true, that takes the dependecies one-by-one and unpacks them in respective directories with JOGL-compatible names.
The assembly plugin should then finally ZIP all of it into one file, I use ZIP but I guess it could use JAR packaging also - haven't tried that.

So I guess dependecySets is the solution, that's why there never was a file mapper.

BTW, Ant+Ivy is still the best build system for java IMHO