title: maven assembly - jar misses own classes
body: <p>I want to create a jar file from a maven project. I need to use an own assembly.xml because I need to exclude a few .so files:</p>
  
  <p>assembly.xml</p>
  
  <pre><code>&lt;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"&gt;
  
    &lt;id&gt;assembly-with-so&lt;/id&gt;
    &lt;formats&gt;
      &lt;format&gt;jar&lt;/format&gt;
    &lt;/formats&gt;
    &lt;includeBaseDirectory&gt;false&lt;/includeBaseDirectory&gt;
    &lt;dependencySets&gt;
      &lt;!-- package the regular dependencies --&gt;
      &lt;dependencySet&gt;
        &lt;outputDirectory&gt;/&lt;/outputDirectory&gt;
        &lt;useProjectArtifact&gt;true&lt;/useProjectArtifact&gt;
        &lt;unpack&gt;true&lt;/unpack&gt;
        &lt;scope&gt;runtime&lt;/scope&gt;
        &lt;excludes&gt;
          &lt;exclude&gt;jcuda:libJCublas:so:linux-x86_64:0.6.5&lt;/exclude&gt;
          [...]
        &lt;/excludes&gt;
      &lt;/dependencySet&gt;
      &lt;dependencySet&gt;
        &lt;outputDirectory&gt;/&lt;/outputDirectory&gt;
        &lt;includes&gt;
          &lt;include&gt;jcuda:libJCublas:so:linux-x86_64:0.6.5&lt;/include&gt;
          [...]
        &lt;/includes&gt;
      &lt;/dependencySet&gt;
    &lt;/dependencySets&gt;
  &lt;/assembly&gt;
  </code></pre>
  
  <p>pom.xml</p>
  
  <pre><code>[...]
  &lt;build&gt;
      &lt;plugins&gt;
          &lt;plugin&gt;
              &lt;groupId&gt;org.apache.maven.plugins&lt;/groupId&gt;
              &lt;artifactId&gt;maven-assembly-plugin&lt;/artifactId&gt;
              &lt;executions&gt;
                  &lt;execution&gt;
                      &lt;id&gt;jar-with-dependencies&lt;/id&gt;
                      &lt;phase&gt;prepare-package&lt;/phase&gt;
                      &lt;goals&gt;
                          &lt;goal&gt;single&lt;/goal&gt;
                      &lt;/goals&gt;
                  &lt;/execution&gt;
              &lt;/executions&gt;
              &lt;configuration&gt;
                  &lt;descriptor&gt;src/main/assembly/assembly.xml&lt;/descriptor&gt;
                  &lt;appendAssemblyId&gt;false&lt;/appendAssemblyId&gt;
                  &lt;archive&gt;
                      &lt;manifest&gt;
                          &lt;mainClass&gt;org.test.Test&lt;/mainClass&gt;
                      &lt;/manifest&gt;
                  &lt;/archive&gt;
              &lt;/configuration&gt;
          &lt;/plugin&gt;
          [...]
  &lt;/build&gt;
  </code></pre>
  
  <p>When I start the jar file using <code>java -jar File.jar</code> I'm getting the error that the class <code>org.test.Test</code> is missing. When I open the .jar file to have a look what's in it, I see that every file of the dependencies are there but the files of the main project are missing.</p>