So what I wanted todo is rather simple, build an archive containing all my classes, a generated manifest and make it executeable.
10 minutes later we found the solution:
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<executions>
<execution>
<id>convert-to-asci</id>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
<configuration>
<archive>
<manifest>
<mainClass>edu.ucdavis.fiehnlab.alchemy.core.process.util.ConvertMZXmlToAscii</mainClass>
<packageName>edu.ucdavis.fiehnlab.alchemy.core.process.util</packageName>
<addClasspath>true</addClasspath>
</manifest>
</archive>
<descriptors>
<descriptor>src/main/descriptor/jar.xml</descriptor>
</descriptors>
<finalName>ConvertMzXmlToASCII-${project.version}</finalName>
<appendAssemblyId>false</appendAssemblyId>
</configuration>
</execution>
<execution>
<id>alchemy-converter-zip</id>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
<configuration>
<descriptors>
<descriptor>src/main/descriptor/zip.xml</descriptor>
</descriptors>
<attach>true</attach>
<finalName>alchemy-converter-${project.version}</finalName>
</configuration>
</execution>
</executions>
</plugin>
The important part is to set the appendAssembyId to false, otherwise you get all kinds of annoying exceptions....
