Making maven copy additional files inside the build jar (not resources but any file inside any package)?

You can modify the resources section of the <build> bit of the POM:

<resources>
  <resource>
    <directory>src/main/resources</directory>
  </resource>
  <resource>
    <filtering>false</filtering>
    <directory>src/main/java</directory>
    <includes>
      <include>*.rb</include>
    </includes>
    <excludes>
      <exclude>**/*.java</exclude>
    </excludes>
  </resource>
</resources>

Or, the other answer (create the same package structure in src/main/resources) will also work.

Not sure if i understood the problem correctly, but if your Ruby files are packaged by maven and declared as a dependency, you can use the shade plugin to include the contents into the resulting jar file:

<plugin>
    <groupId>org.apache.maven.plugins</groupId>
    <artifactId>maven-shade-plugin</artifactId>
    <version>1.4</version>
    <executions>
        <execution>
            <phase>package</phase>
            <goals>
                <goal>shade</goal>
            </goals>
            <configuration>
                <artifactSet>
                    <includes>
                        <include>org.myapp.mypackage:mypackage</include>
                    </includes>
                </artifactSet>
                <filters>
                    <filter>
                        <artifact>org.myapp.mypackage:mypackage</artifact>
                        <includes>
                            <include>org/my/package/*.rb</include>
                        </includes>
                    </filter>
                </filters>
            </configuration>
        </execution>
    </executions>
</plugin>