Added a compile time script to enforce utils/engine/tools separation.

pom.xml

@@ -32,6 +32,7 @@
         <resource.bundle.skip>false</resource.bundle.skip>
         <!-- TODO: Need a better a way to say "don't include hidden" by default -->
         <gatkdocs.include.hidden>-build-timestamp "${maven.build.timestamp}"</gatkdocs.include.hidden>
+        <gatk.shell.directory>${gatk.basedir}/public/src/main/scripts/shell</gatk.shell.directory>
 
         <!--
         Phases of the build that may be disabled to speed up compilation.
@@ -623,6 +624,21 @@
                 <groupId>org.codehaus.mojo</groupId>
                 <artifactId>exec-maven-plugin</artifactId>
                 <executions>
+                    <execution>
+                        <!--
+                        TODO: Separate maven modules into separate git repos?
+                        Until then, keep devs from accidentally mixing utils/engine/tools.
+                        -->
+                        <id>check-utils-engine-tools</id>
+                        <goals>
+                            <goal>exec</goal>
+                        </goals>
+                        <phase>process-sources</phase>
+                        <inherited>false</inherited>
+                        <configuration>
+                            <executable>${gatk.shell.directory}/check_utils_engine_tools.sh</executable>
+                        </configuration>
+                    </execution>
                     <execution>
                         <!--
                         TODO: Remove after 3.3+ release.
@@ -636,7 +652,7 @@
                         <phase>process-test-resources</phase>
                         <inherited>false</inherited>
                         <configuration>
-                            <executable>${gatk.basedir}/public/src/main/scripts/shell/delete_maven_links.sh</executable>
+                            <executable>${gatk.shell.directory}/delete_maven_links.sh</executable>
                         </configuration>
                     </execution>
                 </executions>

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

@@ -0,0 +1,25 @@
+#!/bin/sh
+
+# Exit with an error if:
+# - utils contains a reference to engine or tools
+# - engine contains a reference to tools
+
+sh -c \
+    "grep -Rn \
+      -e 'org.broadinstitute.gatk.tools' \
+      -e 'org.broadinstitute.gatk.engine' \
+      */*/src/*/*/org/broadinstitute/gatk/utils | \
+      grep -v dependencyanalyzer && \
+    grep -Rn \
+      -e 'org.broadinstitute.gatk.tools' \
+      */*/src/*/*/org/broadinstitute/gatk/engine" | \
+  sed -e 's/:/:'$'\x1B\x5B\x35\x6d''/2' -e 's/$/'$'\x1B\x5B\x6d''/' | \
+  grep gatk
+
+RESULT=$?
+if [[ ${RESULT} -eq 0 ]]; then
+    echo "Fix the above errors. Do not import tools nor engine into the utils, and do not import tools into the engine." >&2
+    exit 1
+else
+    exit 0
+fi