How do I exclude certain target output sub-directories with maven-assembly-plugin?

Question

I am using Maven 3.x with the maven-assembly-plugin. When I build my project I get the message below.

Caused by: org.apache.maven.lifecycle.LifecycleExecutionException: 
Failed to execute goal org.apache.maven.plugins:maven-assembly-plugin:2.2.1:single (tarball) 
on project [ProjectName]: Failed to create assembly: 
Error adding file 'io.something:artifactid:jar:1.5.0' to archive: 
/path/to/project/target/scoverage-classes isn't a file.

I am using scoverage for Scala compilation and testing, and I don't know why the maven-assembly-plugin would want to include that sub-directory.

The project is quite complicated ("highly nested" maven projects), but I will post the relevant parts. In the build plugins section.

<plugin>
    <groupId>org.apache.maven.plugins</groupId>
    <artifactId>maven-assembly-plugin</artifactId>
    <version>2.2.1</version>
    <configuration>
        <tarLongFileMode>gnu</tarLongFileMode>
        <descriptors>
            <descriptor>src/main/assembly/job.xml</descriptor>
            <descriptor>src/main/assembly/src.xml</descriptor>
        </descriptors>
        <archive>
            <index>true</index>
        </archive>
    </configuration>
    <executions>
        <execution>
            <id>tarball</id>
            <phase>package</phase>
            <goals>
                <goal>single</goal>
            </goals>
        </execution>
    </executions>
</plugin>
<plugin>
  <groupId>org.scoverage</groupId>
  <artifactId>scoverage-maven-plugin</artifactId>
  <version>1.3.0</version>
</plugin>

In the reporting-plugins section.

<plugin>
  <groupId>org.scoverage</groupId>
  <artifactId>scoverage-maven-plugin</artifactId>
  <version>1.3.0</version>
  <configuration>
    <scalaVersion>2.10.4</scalaVersion>
    <highlighting>true</highlighting>
    <aggregate>true</aggregate>
  </configuration>
  <reportSets>
    <reportSet>
      <reports>
        <report>report</report>
      </reports>
    </reportSet>
  </reportSets>
</plugin>

The job.xml assembly descriptor is as follows. I'm suspecting this descriptor is the primary culprit (with the target referenced).

<assembly
    xmlns:xsi = "http://www.w3.org/2001/XMLSchema-instance"
    xmlns = "http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0"
    xsi:schemaLocation = "http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0 http://maven.apache.org/xsd/assembly-1.1.0.xsd">
    <id>job</id>
    <formats>
        <format>jar</format>
    </formats>
    <includeBaseDirectory>false</includeBaseDirectory>
    <dependencySets>
        <dependencySet>
            <unpack>false</unpack>
            <scope>runtime</scope>
            <outputDirectory>target</outputDirectory>
        </dependencySet>
        <dependencySet>
            <unpack>false</unpack>
            <scope>system</scope>
            <outputDirectory>target</outputDirectory>
            <excludes>
                <exclude>${artifact.groupId}:${artifact.artifactId}</exclude>
            </excludes>
        </dependencySet>
    </dependencySets>
</assembly>

The src.xml assembly descriptor is as follows.

<assembly
    xmlns:xsi = "http://www.w3.org/2001/XMLSchema-instance"
    xmlns = "http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0"
    xsi:schemaLocation = "http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0 http://maven.apache.org/xsd/assembly-1.1.0.xsd">
    <id>dependencies</id>
    <formats>
        <format>dir</format>
    </formats>
    <includeBaseDirectory>false</includeBaseDirectory>
</assembly>