For now, executing the delete_maven_links.sh just ahead of creating the symbolic links during the process-test-resources phase.

Better than running it during the "clean" phase, since these users may not run "mvn clean" before attempting to build.

pom.xml

@@ -741,6 +741,23 @@
 
         <!-- Invoke plugins that always run -->
         <plugins>
+            <plugin>
+                <groupId>org.codehaus.mojo</groupId>
+                <artifactId>exec-maven-plugin</artifactId>
+                <executions>
+                    <execution>
+                        <id>delete-mavens-links</id>
+                        <phase>process-test-resources</phase>
+                        <goals>
+                            <goal>exec</goal>
+                        </goals>
+                        <inherited>false</inherited>
+                        <configuration>
+                            <executable>${gatk.basedir}/public/src/main/scripts/shell/delete_maven_links.sh</executable>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-failsafe-plugin</artifactId>

public/src/main/scripts/shell/delete_maven_links.sh

@@ -0,0 +1,13 @@
+#!/bin/bash
+#
+# Delete symlinks to testdata/qscripts created by maven. This is necessary
+# in cases where "mvn clean" fails to delete these links itself and exits
+# with an error.
+#
+# Should be run from the root directory of your git clone.
+#
+
+find -L . -type l -name testdata -print0 | xargs -0 rm
+find -L . -type l -name qscript -print0 | xargs -0 rm
+
+exit 0