I would suggest to use this kind of assembly descriptor:
<assembly xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2 http://maven.apache.org/xsd/assembly-1.1.2.xsd">
<id>xyz</id>
<formats>
<format>zip</format>
</formats>
<includeBaseDirectory>true</includeBaseDirectory>
<dependencySets>
<dependencySet>
<useProjectArtifact>false</useProjectArtifact>
<useTransitiveDependencies>true</useTransitiveDependencies>
<outputDirectory>lib</outputDirectory>
<unpack>false</unpack>
<excludes>
<exclude>${project.groupId}:*:*</exclude>
</excludes>
</dependencySet>
</dependencySets>
<moduleSets>
<moduleSet>
<useAllReactorProjects>true</useAllReactorProjects>
<binaries>
<outputDirectory>modules</outputDirectory>
<unpack>false</unpack>
</binaries>
</moduleSet>
</moduleSets>
</assembly>
Based on your descriptor i would suggest to use <includeBaseDirectory>true</includeBaseDirectory>
cause you prefixed all ouputDirectories with ${artifactId}
.
The above descriptor will create a zip file which contains sub-folders lib which contains the dependencies and a folder modules
which contains the modules of your multi-module build.
Furthermore i would suggest to create a separate module which is responsible for creating the archive.
If your resulting zip contains java source files etc. it sounds you are doing the assembly step within a module which is of packaging jar
.