Remove unused xml code

public/biopet-framework/pom.xml

@@ -49,11 +49,6 @@
             <artifactId>scala-library</artifactId>
             <version>2.11.2</version>
         </dependency>
-<!--        <dependency>
-            <groupId>org.broadinstitute.gatk</groupId>
-            <artifactId>gatk-queue-package-distribution</artifactId>
-            <version>3.3</version>
-        </dependency>-->
         <dependency>
             <groupId>org.broadinstitute.gatk</groupId>
             <artifactId>gatk-queue</artifactId>
@@ -152,52 +147,6 @@
                     </archive>
                 </configuration>
             </plugin>
-<!--            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-shade-plugin</artifactId>
-                <version>2.3</version>
-                <configuration>
-                    <finalName>Biopet-${project.version}-${git.commit.id.abbrev}</finalName>
-                    <transformers>
-                        <transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
-                            <manifestEntries>
-                                <Main-Class>${app.main.class}</Main-Class>
-                                <X-Compile-Source-JDK>${maven.compile.source}</X-Compile-Source-JDK>
-                                <X-Compile-Target-JDK>${maven.compile.target}</X-Compile-Target-JDK>
-                            </manifestEntries>
-                        </transformer>
-                    </transformers>
-                    <filters>
-                        <filter>
-                            <artifact>org.broadinstitute.gatk:gatk-queue-package-distribution</artifact>
-                            <includes>
-                                <include>*/**</include>
-                                <include>org/simpleframework/**</include>
-                                <include>org/jets3t/**</include>
-                                <include>com/sun/**</include>
-                                <include>org/ggf/**</include>
-                                <include>picard/**</include>
-                                <include>htsjdk/**</include>
-                                <include>javassist/**</include>
-                                <include>com/google/**</include>
-                                <include>org/reflections/</include>
-                                <include>org/jgrapht/**</include>
-                                <include>org/broadinstitute/**</include>
-                                <include>org/apache/**</include>
-                                <include>scala/tools/nsc/reporters/**</include>
-                            </includes>
-                        </filter>
-                    </filters>
-                </configuration>
-                <executions>
-                    <execution>
-                        <phase>package</phase>
-                        <goals>
-                            <goal>shade</goal>
-                        </goals>
-                    </execution>
-                </executions>
-            </plugin>-->
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-compiler-plugin</artifactId>