diff --git a/build.xml b/build.xml
index e2ea6e72f..8d4ecbebb 100644
--- a/build.xml
+++ b/build.xml
@@ -11,31 +11,17 @@
   </condition>
 
   <!-- set global properties for this build -->
-  <property name="build" location="build"/>
-  <property name="dist" location="dist"/>
-  <property name="lib"  location="lib"/>
-  <property name="javadoc" location="javadoc" />
-
   <path id="thirdparty.dependencies">
-    <fileset dir="${lib}" includes="*.jar" />
+    <fileset dir="lib" includes="*.jar" />
   </path>
 
-  <path id="core.classpath">
-    <path refid="thirdparty.dependencies" />
-  </path>
-
-  <path id="playground.classpath">
-    <path refid="thirdparty.dependencies" />
-    <fileset dir="${build}" includes="**/*.class" />
-  </path>
-
-  <path id="core.srcdir">
-    <dirset dir="core/java/src"/>
-  </path>
-
-  <path id="playground.srcdir">
-    <path refid="core.srcdir" />
-    <dirset dir="playground/java/src" />
+  <path id="source">
+    <dirset dir="java/src">
+      <patternset>
+        <include name="org/broadinstitute/sting/*" />
+        <exclude name="**/playground/**" unless="target.is.playground" />
+      </patternset>
+    </dirset>
   </path>
 
   <!-- ivy properties -->
@@ -69,79 +55,77 @@
     <echo message="Compiling module ${target}" />
 
     <!-- Create the build directory structure used by compile -->
-    <mkdir dir="${build}" />
+    <mkdir dir="build" />
   </target>
 
   <target name="compile" depends="init,resolve"
           description="compile the source">
-    <!-- Compile the java code from ${src} into ${build} -->
-    <javac destdir="${build}" classpathref="${target}.classpath"
+    <!-- Compile the java code from ${src} into build -->
+    <javac destdir="build" classpathref="thirdparty.dependencies"
            debug="true" debuglevel="lines,vars,source">
-       <src refid="${target}.srcdir" />
+       <src refid="source" />
     </javac>
   </target>
 
   <target name="dist" depends="compile"
           description="generate the distribution" >
-    <mkdir dir="${dist}"/>
+    <mkdir dir="dist"/>
 
-    <copy todir="${dist}">
-      <fileset dir="${lib}" includes="*.jar" />
+    <copy todir="dist">
+      <fileset dir="lib" includes="*.jar" />
     </copy>
 
-    <jar jarfile="${dist}/StingUtils.jar">
-      <fileset dir="${build}" includes="org/broadinstitute/sting/utils/**" />
+    <jar jarfile="dist/StingUtils.jar">
+      <fileset dir="build" includes="**/utils/**/*.class" />
     </jar>
 
-    <jar jarfile="${dist}/GenomeAnalysisTK.jar">
-      <fileset dir="${build}" includes="org/broadinstitute/sting/gatk/**" />
+    <jar jarfile="dist/GenomeAnalysisTK.jar">
+      <fileset dir="build" includes="**/gatk/**/*.class" />
       <manifest>
         <attribute name="Main-Class" value="org.broadinstitute.sting.gatk.GenomeAnalysisTK" />
       </manifest>
     </jar>
 
-    <!-- Call special distribution methods for the playground.  Will not run if target isn't playground -->  
-    <antcall target="dist.playground"/>
-
-    <pathconvert property="jar.classpath" pathsep=" ">
-      <flattenmapper />
-      <fileset dir="${dist}" includes="*.jar" />
-    </pathconvert>
-
-    <jar jarfile="${dist}/StingUtils.jar" update="true">
+    <jar jarfile="dist/FourBaseCaller.jar" whenmanifestonly="skip">
+      <fileset dir="build" includes="**/fourbasecaller/**/*.class" />
       <manifest>
-        <attribute name="Class-Path" value="${jar.classpath}" />
+        <attribute name="Main-Class" value="org.broadinstitute.sting.playground.fourbasecaller.FourBaseCaller" />
       </manifest>
     </jar>
 
-    <jar jarfile="${dist}/GenomeAnalysisTK.jar" update="true">
-      <manifest>
-        <attribute name="Class-Path" value="${jar.classpath}" />
-      </manifest>
-    </jar>
-
-    <jar jarfile="${dist}/FourBaseCaller.jar" basedir="${build}">
-      <manifest>
-        <attribute name="Class-Path" value="${jar.classpath}" />
-        <attribute name="Main-Class" value="org.broadinstitute.sting.projects.fourbasecaller.FourBaseCaller" />
-      </manifest>
-    </jar>
-  </target>
-
-  <target name="dist.playground" if="target.is.playground">
-    <jar jarfile="${dist}/Playground.jar">
-      <fileset dir="${build}">
-        <exclude name="org/broadinstitute/sting/utils/**" />
-        <exclude name="org/broadinstitute/sting/gatk/**" />
+    <jar jarfile="dist/Playground.jar" whenmanifestonly="skip">
+      <fileset dir="build">
+        <include name="**/*.class" />
+        <exclude name="**/utils/**" />
+        <exclude name="**/gatk/**" />
+        <exclude name="**/fourbasecaller/**" />
       </fileset>
     </jar>
 
     <pathconvert property="jar.classpath" pathsep=" ">
       <flattenmapper />
-      <fileset dir="${dist}" includes="*.jar" />
+      <fileset dir="dist" includes="*.jar" />
     </pathconvert>
 
-    <jar jarfile="${dist}/Playground.jar" update="true">
+    <jar jarfile="dist/StingUtils.jar" update="true">
+      <manifest>
+        <attribute name="Class-Path" value="${jar.classpath}" />
+      </manifest>
+    </jar>
+
+    <jar jarfile="dist/GenomeAnalysisTK.jar" update="true">
+      <manifest>
+        <attribute name="Class-Path" value="${jar.classpath}" />
+      </manifest>
+    </jar>
+
+    <jar jarfile="dist/FourBaseCaller.jar" update="true" whenmanifestonly="skip">
+      <manifest>
+        <attribute name="Class-Path" value="${jar.classpath}" />
+      </manifest>
+    </jar>
+
+    <jar jarfile="dist/Playground.jar" update="true" whenmanifestonly="skip">
       <manifest>
         <attribute name="Class-Path" value="${jar.classpath}" />
       </manifest>
@@ -149,14 +133,15 @@
   </target>
 
   <target name="javadoc">
-    <mkdir dir="${javadoc}" />
-    <javadoc sourcepathref="${target}.srcdir" destdir="${javadoc}" />
+    <mkdir dir="javadoc" />
+    <javadoc sourcepathref="${target}.srcdir" destdir="javadoc" />
   </target>
 
   <target name="clean"
           description="clean up" >
-    <delete dir="${build}"/>
-    <delete dir="${dist}"/>
-    <delete dir="${lib}" />
+    <delete dir="out" />
+    <delete dir="build" />
+    <delete dir="dist" />
+    <delete dir="lib" />
   </target>
 </project>
diff --git a/core/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
similarity index 100%
rename from core/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
rename to java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
diff --git a/core/java/src/org/broadinstitute/sting/gatk/LocusContext.java b/java/src/org/broadinstitute/sting/gatk/LocusContext.java
similarity index 100%
rename from core/java/src/org/broadinstitute/sting/gatk/LocusContext.java
rename to java/src/org/broadinstitute/sting/gatk/LocusContext.java
diff --git a/core/java/src/org/broadinstitute/sting/gatk/TraversalEngine.java b/java/src/org/broadinstitute/sting/gatk/TraversalEngine.java
similarity index 100%
rename from core/java/src/org/broadinstitute/sting/gatk/TraversalEngine.java
rename to java/src/org/broadinstitute/sting/gatk/TraversalEngine.java
diff --git a/core/java/src/org/broadinstitute/sting/gatk/WalkerManager.java b/java/src/org/broadinstitute/sting/gatk/WalkerManager.java
similarity index 100%
rename from core/java/src/org/broadinstitute/sting/gatk/WalkerManager.java
rename to java/src/org/broadinstitute/sting/gatk/WalkerManager.java
diff --git a/core/java/src/org/broadinstitute/sting/gatk/iterators/LocusIterator.java b/java/src/org/broadinstitute/sting/gatk/iterators/LocusIterator.java
similarity index 100%
rename from core/java/src/org/broadinstitute/sting/gatk/iterators/LocusIterator.java
rename to java/src/org/broadinstitute/sting/gatk/iterators/LocusIterator.java
diff --git a/core/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByHanger.java b/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByHanger.java
similarity index 100%
rename from core/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByHanger.java
rename to java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByHanger.java
diff --git a/core/java/src/org/broadinstitute/sting/gatk/iterators/PushbackIterator.java b/java/src/org/broadinstitute/sting/gatk/iterators/PushbackIterator.java
similarity index 100%
rename from core/java/src/org/broadinstitute/sting/gatk/iterators/PushbackIterator.java
rename to java/src/org/broadinstitute/sting/gatk/iterators/PushbackIterator.java
diff --git a/core/java/src/org/broadinstitute/sting/gatk/iterators/ReferenceIterator.java b/java/src/org/broadinstitute/sting/gatk/iterators/ReferenceIterator.java
similarity index 100%
rename from core/java/src/org/broadinstitute/sting/gatk/iterators/ReferenceIterator.java
rename to java/src/org/broadinstitute/sting/gatk/iterators/ReferenceIterator.java
diff --git a/core/java/src/org/broadinstitute/sting/gatk/iterators/SamQueryIterator.java b/java/src/org/broadinstitute/sting/gatk/iterators/SamQueryIterator.java
similarity index 100%
rename from core/java/src/org/broadinstitute/sting/gatk/iterators/SamQueryIterator.java
rename to java/src/org/broadinstitute/sting/gatk/iterators/SamQueryIterator.java
diff --git a/core/java/src/org/broadinstitute/sting/gatk/iterators/SortSamIterator.java b/java/src/org/broadinstitute/sting/gatk/iterators/SortSamIterator.java
similarity index 100%
rename from core/java/src/org/broadinstitute/sting/gatk/iterators/SortSamIterator.java
rename to java/src/org/broadinstitute/sting/gatk/iterators/SortSamIterator.java
diff --git a/core/java/src/org/broadinstitute/sting/gatk/iterators/ThreadedIterator.java b/java/src/org/broadinstitute/sting/gatk/iterators/ThreadedIterator.java
similarity index 100%
rename from core/java/src/org/broadinstitute/sting/gatk/iterators/ThreadedIterator.java
rename to java/src/org/broadinstitute/sting/gatk/iterators/ThreadedIterator.java
diff --git a/core/java/src/org/broadinstitute/sting/gatk/iterators/VerifyingSamIterator.java b/java/src/org/broadinstitute/sting/gatk/iterators/VerifyingSamIterator.java
similarity index 100%
rename from core/java/src/org/broadinstitute/sting/gatk/iterators/VerifyingSamIterator.java
rename to java/src/org/broadinstitute/sting/gatk/iterators/VerifyingSamIterator.java
diff --git a/core/java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedData.java b/java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedData.java
similarity index 100%
rename from core/java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedData.java
rename to java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedData.java
diff --git a/core/java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedDatum.java b/java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedDatum.java
similarity index 100%
rename from core/java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedDatum.java
rename to java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedDatum.java
diff --git a/core/java/src/org/broadinstitute/sting/gatk/refdata/rodDbSNP.java b/java/src/org/broadinstitute/sting/gatk/refdata/rodDbSNP.java
similarity index 100%
rename from core/java/src/org/broadinstitute/sting/gatk/refdata/rodDbSNP.java
rename to java/src/org/broadinstitute/sting/gatk/refdata/rodDbSNP.java
diff --git a/core/java/src/org/broadinstitute/sting/gatk/refdata/rodGFF.java b/java/src/org/broadinstitute/sting/gatk/refdata/rodGFF.java
similarity index 100%
rename from core/java/src/org/broadinstitute/sting/gatk/refdata/rodGFF.java
rename to java/src/org/broadinstitute/sting/gatk/refdata/rodGFF.java
diff --git a/core/java/src/org/broadinstitute/sting/gatk/walkers/BasicLociWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/BasicLociWalker.java
similarity index 100%
rename from core/java/src/org/broadinstitute/sting/gatk/walkers/BasicLociWalker.java
rename to java/src/org/broadinstitute/sting/gatk/walkers/BasicLociWalker.java
diff --git a/core/java/src/org/broadinstitute/sting/gatk/walkers/BasicReadWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/BasicReadWalker.java
similarity index 100%
rename from core/java/src/org/broadinstitute/sting/gatk/walkers/BasicReadWalker.java
rename to java/src/org/broadinstitute/sting/gatk/walkers/BasicReadWalker.java
diff --git a/core/java/src/org/broadinstitute/sting/gatk/walkers/CountLociWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/CountLociWalker.java
similarity index 100%
rename from core/java/src/org/broadinstitute/sting/gatk/walkers/CountLociWalker.java
rename to java/src/org/broadinstitute/sting/gatk/walkers/CountLociWalker.java
diff --git a/core/java/src/org/broadinstitute/sting/gatk/walkers/CountReadsWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/CountReadsWalker.java
similarity index 100%
rename from core/java/src/org/broadinstitute/sting/gatk/walkers/CountReadsWalker.java
rename to java/src/org/broadinstitute/sting/gatk/walkers/CountReadsWalker.java
diff --git a/core/java/src/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageWalker.java
similarity index 100%
rename from core/java/src/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageWalker.java
rename to java/src/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageWalker.java
diff --git a/core/java/src/org/broadinstitute/sting/gatk/walkers/LocusWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/LocusWalker.java
similarity index 100%
rename from core/java/src/org/broadinstitute/sting/gatk/walkers/LocusWalker.java
rename to java/src/org/broadinstitute/sting/gatk/walkers/LocusWalker.java
diff --git a/core/java/src/org/broadinstitute/sting/gatk/walkers/NullWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/NullWalker.java
similarity index 100%
rename from core/java/src/org/broadinstitute/sting/gatk/walkers/NullWalker.java
rename to java/src/org/broadinstitute/sting/gatk/walkers/NullWalker.java
diff --git a/core/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java
similarity index 100%
rename from core/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java
rename to java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java
diff --git a/core/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java
similarity index 100%
rename from core/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java
rename to java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java
diff --git a/core/java/src/org/broadinstitute/sting/gatk/walkers/ReadWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/ReadWalker.java
similarity index 100%
rename from core/java/src/org/broadinstitute/sting/gatk/walkers/ReadWalker.java
rename to java/src/org/broadinstitute/sting/gatk/walkers/ReadWalker.java
diff --git a/core/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java b/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java
similarity index 100%
rename from core/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java
rename to java/src/org/broadinstitute/sting/gatk/walkers/Walker.java
diff --git a/playground/java/src/org/broadinstitute/sting/ValidateSAM.java b/java/src/org/broadinstitute/sting/playground/ValidateSAM.java
similarity index 98%
rename from playground/java/src/org/broadinstitute/sting/ValidateSAM.java
rename to java/src/org/broadinstitute/sting/playground/ValidateSAM.java
index 2fac251f9..4d4344358 100755
--- a/playground/java/src/org/broadinstitute/sting/ValidateSAM.java
+++ b/java/src/org/broadinstitute/sting/playground/ValidateSAM.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting;
+package org.broadinstitute.sting.playground.playground;
 
 import net.sf.samtools.*;
 import net.sf.samtools.SAMFileReader.ValidationStringency;
diff --git a/playground/java/src/org/broadinstitute/sting/projects/fourbasecaller/FourBaseCaller.java b/java/src/org/broadinstitute/sting/playground/fourbasecaller/FourBaseCaller.java
similarity index 97%
rename from playground/java/src/org/broadinstitute/sting/projects/fourbasecaller/FourBaseCaller.java
rename to java/src/org/broadinstitute/sting/playground/fourbasecaller/FourBaseCaller.java
index 38f54acb5..ebc749cc0 100644
--- a/playground/java/src/org/broadinstitute/sting/projects/fourbasecaller/FourBaseCaller.java
+++ b/java/src/org/broadinstitute/sting/playground/fourbasecaller/FourBaseCaller.java
@@ -1,11 +1,11 @@
-package org.broadinstitute.sting.projects.fourbasecaller;
+package org.broadinstitute.sting.playground.fourbasecaller;
 
 import java.io.File;
 import java.util.Vector;
 import java.lang.Math;
 
-import org.broadinstitute.sting.illumina.FirecrestFileParser;
-import org.broadinstitute.sting.illumina.FourIntensity;
+import org.broadinstitute.sting.playground.illumina.FirecrestFileParser;
+import org.broadinstitute.sting.playground.illumina.FourIntensity;
 import cern.colt.matrix.linalg.Algebra;
 import cern.colt.matrix.DoubleMatrix1D;
 import cern.colt.matrix.DoubleFactory1D;
diff --git a/playground/java/src/org/broadinstitute/sting/projects/fourbasecaller/ManyNucleotideSequences.java b/java/src/org/broadinstitute/sting/playground/fourbasecaller/ManyNucleotideSequences.java
similarity index 91%
rename from playground/java/src/org/broadinstitute/sting/projects/fourbasecaller/ManyNucleotideSequences.java
rename to java/src/org/broadinstitute/sting/playground/fourbasecaller/ManyNucleotideSequences.java
index ca2ffe28f..52238fbe2 100644
--- a/playground/java/src/org/broadinstitute/sting/projects/fourbasecaller/ManyNucleotideSequences.java
+++ b/java/src/org/broadinstitute/sting/playground/fourbasecaller/ManyNucleotideSequences.java
@@ -1,9 +1,9 @@
-package org.broadinstitute.sting.projects.fourbasecaller;
+package org.broadinstitute.sting.playground.fourbasecaller;
 
 import java.io.File;
 import java.util.Vector;
 
-import org.broadinstitute.sting.projects.fourbasecaller.NucleotideSequence;
+import org.broadinstitute.sting.playground.fourbasecaller.NucleotideSequence;
 
 import edu.mit.broad.picard.reference.ReferenceSequence;
 import edu.mit.broad.picard.reference.ReferenceSequenceFile;
diff --git a/playground/java/src/org/broadinstitute/sting/projects/fourbasecaller/Nucleotide.java b/java/src/org/broadinstitute/sting/playground/fourbasecaller/Nucleotide.java
similarity index 92%
rename from playground/java/src/org/broadinstitute/sting/projects/fourbasecaller/Nucleotide.java
rename to java/src/org/broadinstitute/sting/playground/fourbasecaller/Nucleotide.java
index 4921554f4..407a412f6 100644
--- a/playground/java/src/org/broadinstitute/sting/projects/fourbasecaller/Nucleotide.java
+++ b/java/src/org/broadinstitute/sting/playground/fourbasecaller/Nucleotide.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.projects.fourbasecaller;
+package org.broadinstitute.sting.playground.fourbasecaller;
 
 import java.lang.String;
 
diff --git a/playground/java/src/org/broadinstitute/sting/projects/fourbasecaller/NucleotideChannelCovariances.java b/java/src/org/broadinstitute/sting/playground/fourbasecaller/NucleotideChannelCovariances.java
similarity index 93%
rename from playground/java/src/org/broadinstitute/sting/projects/fourbasecaller/NucleotideChannelCovariances.java
rename to java/src/org/broadinstitute/sting/playground/fourbasecaller/NucleotideChannelCovariances.java
index 3b1f85ecc..669188148 100755
--- a/playground/java/src/org/broadinstitute/sting/projects/fourbasecaller/NucleotideChannelCovariances.java
+++ b/java/src/org/broadinstitute/sting/playground/fourbasecaller/NucleotideChannelCovariances.java
@@ -1,9 +1,9 @@
-package org.broadinstitute.sting.projects.fourbasecaller;
+package org.broadinstitute.sting.playground.fourbasecaller;
 
 import cern.colt.matrix.DoubleFactory2D;
 import cern.colt.matrix.DoubleMatrix2D;
 import cern.colt.matrix.linalg.Algebra;
-import org.broadinstitute.sting.illumina.FourIntensity;
+import org.broadinstitute.sting.playground.illumina.FourIntensity;
 
 public class NucleotideChannelCovariances {
     private DoubleMatrix2D[] covs;
diff --git a/playground/java/src/org/broadinstitute/sting/projects/fourbasecaller/NucleotideChannelMeans.java b/java/src/org/broadinstitute/sting/playground/fourbasecaller/NucleotideChannelMeans.java
similarity index 92%
rename from playground/java/src/org/broadinstitute/sting/projects/fourbasecaller/NucleotideChannelMeans.java
rename to java/src/org/broadinstitute/sting/playground/fourbasecaller/NucleotideChannelMeans.java
index 511a6c67e..f07b7e7dc 100755
--- a/playground/java/src/org/broadinstitute/sting/projects/fourbasecaller/NucleotideChannelMeans.java
+++ b/java/src/org/broadinstitute/sting/playground/fourbasecaller/NucleotideChannelMeans.java
@@ -1,6 +1,6 @@
-package org.broadinstitute.sting.projects.fourbasecaller;
+package org.broadinstitute.sting.playground.fourbasecaller;
 
-import org.broadinstitute.sting.illumina.FourIntensity;
+import org.broadinstitute.sting.playground.illumina.FourIntensity;
 
 public class NucleotideChannelMeans {
     private FourIntensity[] sigs;
diff --git a/playground/java/src/org/broadinstitute/sting/projects/fourbasecaller/NucleotideSequence.java b/java/src/org/broadinstitute/sting/playground/fourbasecaller/NucleotideSequence.java
similarity index 93%
rename from playground/java/src/org/broadinstitute/sting/projects/fourbasecaller/NucleotideSequence.java
rename to java/src/org/broadinstitute/sting/playground/fourbasecaller/NucleotideSequence.java
index d4ef5c10b..1b6d7d587 100644
--- a/playground/java/src/org/broadinstitute/sting/projects/fourbasecaller/NucleotideSequence.java
+++ b/java/src/org/broadinstitute/sting/playground/fourbasecaller/NucleotideSequence.java
@@ -1,6 +1,6 @@
-package org.broadinstitute.sting.projects.fourbasecaller;
+package org.broadinstitute.sting.playground.fourbasecaller;
 
-import org.broadinstitute.sting.projects.fourbasecaller.Nucleotide;
+import org.broadinstitute.sting.playground.fourbasecaller.Nucleotide;
 
 import java.lang.String;
 import java.util.Vector;
diff --git a/playground/java/src/org/broadinstitute/sting/gatk/PrepareROD.java b/java/src/org/broadinstitute/sting/playground/gatk/PrepareROD.java
similarity index 98%
rename from playground/java/src/org/broadinstitute/sting/gatk/PrepareROD.java
rename to java/src/org/broadinstitute/sting/playground/gatk/PrepareROD.java
index 4c37a05d1..338aed7b1 100644
--- a/playground/java/src/org/broadinstitute/sting/gatk/PrepareROD.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/PrepareROD.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.gatk;
+package org.broadinstitute.sting.playground.gatk;
 
 import net.sf.samtools.SAMSequenceRecord;
 import edu.mit.broad.picard.cmdline.CommandLineProgram;
diff --git a/playground/java/src/org/broadinstitute/sting/gatk/iterators/SingleLocusIterator.java b/java/src/org/broadinstitute/sting/playground/gatk/iterators/SingleLocusIterator.java
similarity index 98%
rename from playground/java/src/org/broadinstitute/sting/gatk/iterators/SingleLocusIterator.java
rename to java/src/org/broadinstitute/sting/playground/gatk/iterators/SingleLocusIterator.java
index b6037d36f..0300ba1af 100755
--- a/playground/java/src/org/broadinstitute/sting/gatk/iterators/SingleLocusIterator.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/iterators/SingleLocusIterator.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.gatk.iterators;
+package org.broadinstitute.sting.playground.gatk.iterators;
 
 import net.sf.samtools.util.CloseableIterator;
 import net.sf.samtools.SAMRecord;
diff --git a/playground/java/src/org/broadinstitute/sting/gatk/walkers/AlignedReadsHistoWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/AlignedReadsHistoWalker.java
similarity index 93%
rename from playground/java/src/org/broadinstitute/sting/gatk/walkers/AlignedReadsHistoWalker.java
rename to java/src/org/broadinstitute/sting/playground/gatk/walkers/AlignedReadsHistoWalker.java
index 01be7686c..c7e5fa529 100755
--- a/playground/java/src/org/broadinstitute/sting/gatk/walkers/AlignedReadsHistoWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/AlignedReadsHistoWalker.java
@@ -1,7 +1,7 @@
-package org.broadinstitute.sting.gatk.walkers;
+package org.broadinstitute.sting.playground.gatk.walkers;
 
 import net.sf.samtools.SAMRecord;
-import org.broadinstitute.sting.gatk.walkers.ReadWalker;
+import org.broadinstitute.sting.gatk.walkers.BasicReadWalker;
 import org.broadinstitute.sting.gatk.LocusContext;
 
 /**
diff --git a/playground/java/src/org/broadinstitute/sting/gatk/walkers/AlleleFrequencyMetricsWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyMetricsWalker.java
similarity index 94%
rename from playground/java/src/org/broadinstitute/sting/gatk/walkers/AlleleFrequencyMetricsWalker.java
rename to java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyMetricsWalker.java
index 6357640e9..e3eee8e5e 100755
--- a/playground/java/src/org/broadinstitute/sting/gatk/walkers/AlleleFrequencyMetricsWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyMetricsWalker.java
@@ -1,11 +1,11 @@
-package org.broadinstitute.sting.gatk.walkers;
+package org.broadinstitute.sting.playground.gatk.walkers;
 
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
-import org.broadinstitute.sting.gatk.walkers.AlleleFrequencyWalker;
 import org.broadinstitute.sting.gatk.walkers.BasicLociWalker;
 import org.broadinstitute.sting.gatk.LocusContext;
-import org.broadinstitute.sting.utils.AlleleFrequencyEstimate;
+import org.broadinstitute.sting.playground.gatk.walkers.AlleleFrequencyWalker;
+import org.broadinstitute.sting.playground.utils.AlleleFrequencyEstimate;
 
 import java.util.List;
 
diff --git a/playground/java/src/org/broadinstitute/sting/gatk/walkers/AlleleFrequencyWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyWalker.java
similarity index 98%
rename from playground/java/src/org/broadinstitute/sting/gatk/walkers/AlleleFrequencyWalker.java
rename to java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyWalker.java
index f81fd102b..870225dde 100755
--- a/playground/java/src/org/broadinstitute/sting/gatk/walkers/AlleleFrequencyWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyWalker.java
@@ -1,10 +1,10 @@
-package org.broadinstitute.sting.gatk.walkers;
+package org.broadinstitute.sting.playground.gatk.walkers;
 //import org.broadinstitute.sting.gatk.iterators.LocusIterator;
 import org.broadinstitute.sting.gatk.LocusContext;
-import org.broadinstitute.sting.utils.AlleleFrequencyEstimate;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
-import org.broadinstitute.sting.utils.AlleleFrequencyEstimate;
+import org.broadinstitute.sting.gatk.walkers.BasicLociWalker;
+import org.broadinstitute.sting.playground.utils.AlleleFrequencyEstimate;
 import net.sf.samtools.SAMRecord;
 
 import java.util.List;
diff --git a/playground/java/src/org/broadinstitute/sting/gatk/walkers/BaseQualityDumpWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseQualityDumpWalker.java
similarity index 93%
rename from playground/java/src/org/broadinstitute/sting/gatk/walkers/BaseQualityDumpWalker.java
rename to java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseQualityDumpWalker.java
index edbaf47ab..43db5f71e 100755
--- a/playground/java/src/org/broadinstitute/sting/gatk/walkers/BaseQualityDumpWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseQualityDumpWalker.java
@@ -1,7 +1,8 @@
-package org.broadinstitute.sting.gatk.walkers;
+package org.broadinstitute.sting.playground.gatk.walkers;
 
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.LocusContext;
+import org.broadinstitute.sting.gatk.walkers.BasicReadWalker;
 import org.broadinstitute.sting.utils.Utils;
 import edu.mit.broad.picard.reference.ReferenceSequence;
 
@@ -51,4 +52,4 @@ public class BaseQualityDumpWalker extends BasicReadWalker<Integer, Integer> {
     public Integer reduce(Integer value, Integer sum) {
         return value + sum;
     }
-}
\ No newline at end of file
+}
diff --git a/playground/java/src/org/broadinstitute/sting/gatk/walkers/BaseQualityHistoWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseQualityHistoWalker.java
similarity index 93%
rename from playground/java/src/org/broadinstitute/sting/gatk/walkers/BaseQualityHistoWalker.java
rename to java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseQualityHistoWalker.java
index f1b84cac8..5742c070c 100755
--- a/playground/java/src/org/broadinstitute/sting/gatk/walkers/BaseQualityHistoWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseQualityHistoWalker.java
@@ -1,7 +1,7 @@
-package org.broadinstitute.sting.gatk.walkers;
+package org.broadinstitute.sting.playground.gatk.walkers;
 
 import net.sf.samtools.SAMRecord;
-import org.broadinstitute.sting.gatk.walkers.ReadWalker;
+import org.broadinstitute.sting.gatk.walkers.BasicReadWalker;
 import org.broadinstitute.sting.gatk.LocusContext;
 
 /**
diff --git a/playground/java/src/org/broadinstitute/sting/gatk/walkers/MismatchCounterWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/MismatchCounterWalker.java
similarity index 92%
rename from playground/java/src/org/broadinstitute/sting/gatk/walkers/MismatchCounterWalker.java
rename to java/src/org/broadinstitute/sting/playground/gatk/walkers/MismatchCounterWalker.java
index 64ae49dbf..c5b2f851f 100755
--- a/playground/java/src/org/broadinstitute/sting/gatk/walkers/MismatchCounterWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/MismatchCounterWalker.java
@@ -1,7 +1,8 @@
-package org.broadinstitute.sting.gatk.walkers;
+package org.broadinstitute.sting.playground.gatk.walkers;
 
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.LocusContext;
+import org.broadinstitute.sting.gatk.walkers.BasicReadWalker;
 import org.broadinstitute.sting.utils.Utils;
 import edu.mit.broad.picard.reference.ReferenceSequence;
 
@@ -42,4 +43,4 @@ public class MismatchCounterWalker extends BasicReadWalker<Integer, Integer> {
     public Integer reduce(Integer value, Integer sum) {
         return value + sum;
     }
-}
\ No newline at end of file
+}
diff --git a/playground/java/src/org/broadinstitute/sting/gatk/walkers/MismatchHistoWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/MismatchHistoWalker.java
similarity index 96%
rename from playground/java/src/org/broadinstitute/sting/gatk/walkers/MismatchHistoWalker.java
rename to java/src/org/broadinstitute/sting/playground/gatk/walkers/MismatchHistoWalker.java
index 4e0b7cbc0..eb910e04c 100755
--- a/playground/java/src/org/broadinstitute/sting/gatk/walkers/MismatchHistoWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/MismatchHistoWalker.java
@@ -1,7 +1,8 @@
-package org.broadinstitute.sting.gatk.walkers;
+package org.broadinstitute.sting.playground.gatk.walkers;
 
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.LocusContext;
+import org.broadinstitute.sting.gatk.walkers.BasicReadWalker;
 import org.broadinstitute.sting.utils.Utils;
 import edu.mit.broad.picard.reference.ReferenceSequence;
 
@@ -85,4 +86,4 @@ public class MismatchHistoWalker extends BasicReadWalker<Integer, Integer> {
             System.arraycopy (oldArray,0,newArray,0,preserveLength);
         return newArray;
     }
-}
\ No newline at end of file
+}
diff --git a/playground/java/src/org/broadinstitute/sting/gatk/walkers/SingleSampleGenotyper.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/SingleSampleGenotyper.java
similarity index 97%
rename from playground/java/src/org/broadinstitute/sting/gatk/walkers/SingleSampleGenotyper.java
rename to java/src/org/broadinstitute/sting/playground/gatk/walkers/SingleSampleGenotyper.java
index 3b483f6c1..1459e8b18 100644
--- a/playground/java/src/org/broadinstitute/sting/gatk/walkers/SingleSampleGenotyper.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/SingleSampleGenotyper.java
@@ -1,8 +1,9 @@
-package org.broadinstitute.sting.gatk.walkers;
+package org.broadinstitute.sting.playground.gatk.walkers;
 
 import org.broadinstitute.sting.gatk.LocusContext;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
+import org.broadinstitute.sting.gatk.walkers.BasicLociWalker;
 import org.broadinstitute.sting.utils.Utils;
 import net.sf.samtools.SAMRecord;
 
diff --git a/playground/java/src/org/broadinstitute/sting/illumina/AbstractFirecrestFileParser.java b/java/src/org/broadinstitute/sting/playground/illumina/AbstractFirecrestFileParser.java
similarity index 98%
rename from playground/java/src/org/broadinstitute/sting/illumina/AbstractFirecrestFileParser.java
rename to java/src/org/broadinstitute/sting/playground/illumina/AbstractFirecrestFileParser.java
index 33620fa55..4dee0a49e 100644
--- a/playground/java/src/org/broadinstitute/sting/illumina/AbstractFirecrestFileParser.java
+++ b/java/src/org/broadinstitute/sting/playground/illumina/AbstractFirecrestFileParser.java
@@ -8,7 +8,7 @@
 * the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
 */
 //package edu.mit.broad.picard.illumina;
-package org.broadinstitute.sting.illumina;
+package org.broadinstitute.sting.playground.illumina;
 
 import edu.mit.broad.picard.util.BasicTextFileParser;
 
diff --git a/playground/java/src/org/broadinstitute/sting/illumina/FirecrestFileParser.java b/java/src/org/broadinstitute/sting/playground/illumina/FirecrestFileParser.java
similarity index 96%
rename from playground/java/src/org/broadinstitute/sting/illumina/FirecrestFileParser.java
rename to java/src/org/broadinstitute/sting/playground/illumina/FirecrestFileParser.java
index 210619221..254b8b88d 100644
--- a/playground/java/src/org/broadinstitute/sting/illumina/FirecrestFileParser.java
+++ b/java/src/org/broadinstitute/sting/playground/illumina/FirecrestFileParser.java
@@ -7,7 +7,7 @@
 * This software is supplied without any warranty or guaranteed support whatsoever. Neither
 * the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
 */
-package org.broadinstitute.sting.illumina;
+package org.broadinstitute.sting.playground.illumina;
 
 import edu.mit.broad.picard.util.PasteParser;
 import edu.mit.broad.picard.util.FormatUtil;
diff --git a/playground/java/src/org/broadinstitute/sting/illumina/FirecrestFilenameComparator.java b/java/src/org/broadinstitute/sting/playground/illumina/FirecrestFilenameComparator.java
similarity index 95%
rename from playground/java/src/org/broadinstitute/sting/illumina/FirecrestFilenameComparator.java
rename to java/src/org/broadinstitute/sting/playground/illumina/FirecrestFilenameComparator.java
index c64afd3e4..ac43fb20e 100644
--- a/playground/java/src/org/broadinstitute/sting/illumina/FirecrestFilenameComparator.java
+++ b/java/src/org/broadinstitute/sting/playground/illumina/FirecrestFilenameComparator.java
@@ -8,7 +8,7 @@
 * the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
 */
 //package edu.mit.broad.picard.illumina;
-package org.broadinstitute.sting.illumina;
+package org.broadinstitute.sting.playground.illumina;
 
 import java.io.File;
 import java.util.Comparator;
diff --git a/playground/java/src/org/broadinstitute/sting/illumina/FirecrestReadData.java b/java/src/org/broadinstitute/sting/playground/illumina/FirecrestReadData.java
similarity index 94%
rename from playground/java/src/org/broadinstitute/sting/illumina/FirecrestReadData.java
rename to java/src/org/broadinstitute/sting/playground/illumina/FirecrestReadData.java
index dd62cc19d..bd8abc979 100644
--- a/playground/java/src/org/broadinstitute/sting/illumina/FirecrestReadData.java
+++ b/java/src/org/broadinstitute/sting/playground/illumina/FirecrestReadData.java
@@ -7,7 +7,7 @@
 * This software is supplied without any warranty or guaranteed support whatsoever. Neither
 * the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
 */
-package org.broadinstitute.sting.illumina;
+package org.broadinstitute.sting.playground.illumina;
 
 /**
  * Holds all the Firecrest-level data we need (so far) about an individual read.
diff --git a/playground/java/src/org/broadinstitute/sting/illumina/FourIntensity.java b/java/src/org/broadinstitute/sting/playground/illumina/FourIntensity.java
similarity index 96%
rename from playground/java/src/org/broadinstitute/sting/illumina/FourIntensity.java
rename to java/src/org/broadinstitute/sting/playground/illumina/FourIntensity.java
index 0bcc50628..928655bb9 100755
--- a/playground/java/src/org/broadinstitute/sting/illumina/FourIntensity.java
+++ b/java/src/org/broadinstitute/sting/playground/illumina/FourIntensity.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.illumina;
+package org.broadinstitute.sting.playground.illumina;
 
 import java.util.StringTokenizer;
 
diff --git a/playground/java/src/org/broadinstitute/sting/indels/ConsensusSequence.java b/java/src/org/broadinstitute/sting/playground/indels/ConsensusSequence.java
similarity index 97%
rename from playground/java/src/org/broadinstitute/sting/indels/ConsensusSequence.java
rename to java/src/org/broadinstitute/sting/playground/indels/ConsensusSequence.java
index 275b2fb34..2847972cd 100644
--- a/playground/java/src/org/broadinstitute/sting/indels/ConsensusSequence.java
+++ b/java/src/org/broadinstitute/sting/playground/indels/ConsensusSequence.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.indels;
+package org.broadinstitute.sting.playground.indels;
 
 import org.broadinstitute.sting.utils.Pair;
 
diff --git a/playground/java/src/org/broadinstitute/sting/indels/DiscardingPileReceiver.java b/java/src/org/broadinstitute/sting/playground/indels/DiscardingPileReceiver.java
similarity index 85%
rename from playground/java/src/org/broadinstitute/sting/indels/DiscardingPileReceiver.java
rename to java/src/org/broadinstitute/sting/playground/indels/DiscardingPileReceiver.java
index 1a7a1047f..6555110f0 100644
--- a/playground/java/src/org/broadinstitute/sting/indels/DiscardingPileReceiver.java
+++ b/java/src/org/broadinstitute/sting/playground/indels/DiscardingPileReceiver.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.indels;
+package org.broadinstitute.sting.playground.indels;
 
 import net.sf.samtools.SAMRecord;
 
diff --git a/playground/java/src/org/broadinstitute/sting/indels/DiscardingReceiver.java b/java/src/org/broadinstitute/sting/playground/indels/DiscardingReceiver.java
similarity index 84%
rename from playground/java/src/org/broadinstitute/sting/indels/DiscardingReceiver.java
rename to java/src/org/broadinstitute/sting/playground/indels/DiscardingReceiver.java
index 981585ac6..fa7d219f4 100644
--- a/playground/java/src/org/broadinstitute/sting/indels/DiscardingReceiver.java
+++ b/java/src/org/broadinstitute/sting/playground/indels/DiscardingReceiver.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.indels;
+package org.broadinstitute.sting.playground.indels;
 
 import net.sf.samtools.SAMRecord;
 
diff --git a/playground/java/src/org/broadinstitute/sting/indels/Indel.java b/java/src/org/broadinstitute/sting/playground/indels/Indel.java
similarity index 98%
rename from playground/java/src/org/broadinstitute/sting/indels/Indel.java
rename to java/src/org/broadinstitute/sting/playground/indels/Indel.java
index a157b30e8..b5ec9b711 100755
--- a/playground/java/src/org/broadinstitute/sting/indels/Indel.java
+++ b/java/src/org/broadinstitute/sting/playground/indels/Indel.java
@@ -1,6 +1,6 @@
-package org.broadinstitute.sting.indels;
+package org.broadinstitute.sting.playground.indels;
 
-import org.broadinstitute.sting.utils.Interval;
+import org.broadinstitute.sting.playground.utils.Interval;
 
 /**  This class represents an indel as an interval with respect to the <i>original</i> reference and, in addition,
  * stores the indel type ( (I)nsertion or (D)eletion ) and can return meaningful event size (see below).
diff --git a/playground/java/src/org/broadinstitute/sting/indels/IndelInspector.java b/java/src/org/broadinstitute/sting/playground/indels/IndelInspector.java
similarity index 99%
rename from playground/java/src/org/broadinstitute/sting/indels/IndelInspector.java
rename to java/src/org/broadinstitute/sting/playground/indels/IndelInspector.java
index 2d1e0e94a..893c1bedf 100755
--- a/playground/java/src/org/broadinstitute/sting/indels/IndelInspector.java
+++ b/java/src/org/broadinstitute/sting/playground/indels/IndelInspector.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.indels;
+package org.broadinstitute.sting.playground.indels;
 
 import java.io.File;
 import java.util.List;
diff --git a/playground/java/src/org/broadinstitute/sting/indels/IndelRecordPileCollector.java b/java/src/org/broadinstitute/sting/playground/indels/IndelRecordPileCollector.java
similarity index 99%
rename from playground/java/src/org/broadinstitute/sting/indels/IndelRecordPileCollector.java
rename to java/src/org/broadinstitute/sting/playground/indels/IndelRecordPileCollector.java
index a378bce11..2caa4cc6a 100755
--- a/playground/java/src/org/broadinstitute/sting/indels/IndelRecordPileCollector.java
+++ b/java/src/org/broadinstitute/sting/playground/indels/IndelRecordPileCollector.java
@@ -1,10 +1,10 @@
-package org.broadinstitute.sting.indels;
+package org.broadinstitute.sting.playground.indels;
 
 import java.util.*;
 
 
-import org.broadinstitute.sting.indels.Indel.IndelType;
-import org.broadinstitute.sting.utils.*;
+import org.broadinstitute.sting.playground.indels.Indel.IndelType;
+import org.broadinstitute.sting.playground.utils.*;
 import net.sf.samtools.*;
 
 /** Ultimately, this class is a splitter for a stream of alignment records. It detects putative indels, or
diff --git a/playground/java/src/org/broadinstitute/sting/indels/IndexedSequence.java b/java/src/org/broadinstitute/sting/playground/indels/IndexedSequence.java
similarity index 97%
rename from playground/java/src/org/broadinstitute/sting/indels/IndexedSequence.java
rename to java/src/org/broadinstitute/sting/playground/indels/IndexedSequence.java
index 424e0f4ca..02b83d100 100755
--- a/playground/java/src/org/broadinstitute/sting/indels/IndexedSequence.java
+++ b/java/src/org/broadinstitute/sting/playground/indels/IndexedSequence.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.indels;
+package org.broadinstitute.sting.playground.indels;
 
 import java.util.ArrayList;
 import java.util.Hashtable;
diff --git a/playground/java/src/org/broadinstitute/sting/indels/IntervalComparator.java b/java/src/org/broadinstitute/sting/playground/indels/IntervalComparator.java
similarity index 80%
rename from playground/java/src/org/broadinstitute/sting/indels/IntervalComparator.java
rename to java/src/org/broadinstitute/sting/playground/indels/IntervalComparator.java
index 68b281420..8e0d38bce 100755
--- a/playground/java/src/org/broadinstitute/sting/indels/IntervalComparator.java
+++ b/java/src/org/broadinstitute/sting/playground/indels/IntervalComparator.java
@@ -1,6 +1,6 @@
-package org.broadinstitute.sting.indels;
+package org.broadinstitute.sting.playground.indels;
 
-import org.broadinstitute.sting.utils.Interval;
+import org.broadinstitute.sting.playground.utils.Interval;
 
 
 public class IntervalComparator implements java.util.Comparator<Interval> {
diff --git a/playground/java/src/org/broadinstitute/sting/indels/KmerCodeIterator.java b/java/src/org/broadinstitute/sting/playground/indels/KmerCodeIterator.java
similarity index 98%
rename from playground/java/src/org/broadinstitute/sting/indels/KmerCodeIterator.java
rename to java/src/org/broadinstitute/sting/playground/indels/KmerCodeIterator.java
index 3e7d189aa..4bce27939 100755
--- a/playground/java/src/org/broadinstitute/sting/indels/KmerCodeIterator.java
+++ b/java/src/org/broadinstitute/sting/playground/indels/KmerCodeIterator.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.indels;
+package org.broadinstitute.sting.playground.indels;
 
 import java.util.Iterator;
 
diff --git a/playground/java/src/org/broadinstitute/sting/indels/MSAColumn.java b/java/src/org/broadinstitute/sting/playground/indels/MSAColumn.java
similarity index 94%
rename from playground/java/src/org/broadinstitute/sting/indels/MSAColumn.java
rename to java/src/org/broadinstitute/sting/playground/indels/MSAColumn.java
index a86ebde78..f95ff3a23 100755
--- a/playground/java/src/org/broadinstitute/sting/indels/MSAColumn.java
+++ b/java/src/org/broadinstitute/sting/playground/indels/MSAColumn.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.indels;
+package org.broadinstitute.sting.playground.indels;
 
 import java.util.List;
 import java.util.ArrayList;
diff --git a/playground/java/src/org/broadinstitute/sting/indels/Matrix.java b/java/src/org/broadinstitute/sting/playground/indels/Matrix.java
similarity index 93%
rename from playground/java/src/org/broadinstitute/sting/indels/Matrix.java
rename to java/src/org/broadinstitute/sting/playground/indels/Matrix.java
index 094f32fc1..ae85ddae0 100755
--- a/playground/java/src/org/broadinstitute/sting/indels/Matrix.java
+++ b/java/src/org/broadinstitute/sting/playground/indels/Matrix.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.indels;
+package org.broadinstitute.sting.playground.indels;
 
 public class Matrix<T> {
 	private int nRows;
diff --git a/playground/java/src/org/broadinstitute/sting/indels/MultipleAlignment.java b/java/src/org/broadinstitute/sting/playground/indels/MultipleAlignment.java
similarity index 99%
rename from playground/java/src/org/broadinstitute/sting/indels/MultipleAlignment.java
rename to java/src/org/broadinstitute/sting/playground/indels/MultipleAlignment.java
index d1ec8ba38..88d759e9e 100755
--- a/playground/java/src/org/broadinstitute/sting/indels/MultipleAlignment.java
+++ b/java/src/org/broadinstitute/sting/playground/indels/MultipleAlignment.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.indels;
+package org.broadinstitute.sting.playground.indels;
 
 import java.util.*;
 import org.broadinstitute.sting.utils.Utils;
diff --git a/playground/java/src/org/broadinstitute/sting/indels/PairwiseAlignment.java b/java/src/org/broadinstitute/sting/playground/indels/PairwiseAlignment.java
similarity index 99%
rename from playground/java/src/org/broadinstitute/sting/indels/PairwiseAlignment.java
rename to java/src/org/broadinstitute/sting/playground/indels/PairwiseAlignment.java
index 14f411a0a..153d10dd0 100755
--- a/playground/java/src/org/broadinstitute/sting/indels/PairwiseAlignment.java
+++ b/java/src/org/broadinstitute/sting/playground/indels/PairwiseAlignment.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.indels;
+package org.broadinstitute.sting.playground.indels;
 
 import java.util.HashSet;
 import java.util.List;
diff --git a/playground/java/src/org/broadinstitute/sting/indels/PileBuilder.java b/java/src/org/broadinstitute/sting/playground/indels/PileBuilder.java
similarity index 99%
rename from playground/java/src/org/broadinstitute/sting/indels/PileBuilder.java
rename to java/src/org/broadinstitute/sting/playground/indels/PileBuilder.java
index a75db65e8..ceb6bf8d6 100755
--- a/playground/java/src/org/broadinstitute/sting/indels/PileBuilder.java
+++ b/java/src/org/broadinstitute/sting/playground/indels/PileBuilder.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.indels;
+package org.broadinstitute.sting.playground.indels;
 
 import net.sf.samtools.SAMRecord;
 
diff --git a/playground/java/src/org/broadinstitute/sting/indels/RecordPileReceiver.java b/java/src/org/broadinstitute/sting/playground/indels/RecordPileReceiver.java
similarity index 87%
rename from playground/java/src/org/broadinstitute/sting/indels/RecordPileReceiver.java
rename to java/src/org/broadinstitute/sting/playground/indels/RecordPileReceiver.java
index 0853b0438..3aab323e3 100644
--- a/playground/java/src/org/broadinstitute/sting/indels/RecordPileReceiver.java
+++ b/java/src/org/broadinstitute/sting/playground/indels/RecordPileReceiver.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.indels;
+package org.broadinstitute.sting.playground.indels;
 
 import net.sf.samtools.SAMRecord;
 
diff --git a/playground/java/src/org/broadinstitute/sting/indels/RecordReceiver.java b/java/src/org/broadinstitute/sting/playground/indels/RecordReceiver.java
similarity index 85%
rename from playground/java/src/org/broadinstitute/sting/indels/RecordReceiver.java
rename to java/src/org/broadinstitute/sting/playground/indels/RecordReceiver.java
index 378fe1fe9..389b0c43f 100644
--- a/playground/java/src/org/broadinstitute/sting/indels/RecordReceiver.java
+++ b/java/src/org/broadinstitute/sting/playground/indels/RecordReceiver.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.indels;
+package org.broadinstitute.sting.playground.indels;
 
 import net.sf.samtools.SAMRecord;
 
diff --git a/playground/java/src/org/broadinstitute/sting/indels/SequencePile.java b/java/src/org/broadinstitute/sting/playground/indels/SequencePile.java
similarity index 99%
rename from playground/java/src/org/broadinstitute/sting/indels/SequencePile.java
rename to java/src/org/broadinstitute/sting/playground/indels/SequencePile.java
index 1e8a206ef..38a94ce4e 100755
--- a/playground/java/src/org/broadinstitute/sting/indels/SequencePile.java
+++ b/java/src/org/broadinstitute/sting/playground/indels/SequencePile.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.indels;
+package org.broadinstitute.sting.playground.indels;
 
 import java.util.List;
 import java.util.ArrayList;
diff --git a/playground/java/src/org/broadinstitute/sting/indels/StrictlyUpperTriangularMatrix.java b/java/src/org/broadinstitute/sting/playground/indels/StrictlyUpperTriangularMatrix.java
similarity index 93%
rename from playground/java/src/org/broadinstitute/sting/indels/StrictlyUpperTriangularMatrix.java
rename to java/src/org/broadinstitute/sting/playground/indels/StrictlyUpperTriangularMatrix.java
index 54f927027..3c7f0c593 100755
--- a/playground/java/src/org/broadinstitute/sting/indels/StrictlyUpperTriangularMatrix.java
+++ b/java/src/org/broadinstitute/sting/playground/indels/StrictlyUpperTriangularMatrix.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.indels;
+package org.broadinstitute.sting.playground.indels;
 
 public class StrictlyUpperTriangularMatrix extends SymmetricMatrix {
 
diff --git a/playground/java/src/org/broadinstitute/sting/indels/SymmetricMatrix.java b/java/src/org/broadinstitute/sting/playground/indels/SymmetricMatrix.java
similarity index 95%
rename from playground/java/src/org/broadinstitute/sting/indels/SymmetricMatrix.java
rename to java/src/org/broadinstitute/sting/playground/indels/SymmetricMatrix.java
index 9a1ec0459..b7c2509da 100644
--- a/playground/java/src/org/broadinstitute/sting/indels/SymmetricMatrix.java
+++ b/java/src/org/broadinstitute/sting/playground/indels/SymmetricMatrix.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.indels;
+package org.broadinstitute.sting.playground.indels;
 
 /**
  * Created by IntelliJ IDEA.
diff --git a/playground/java/src/org/broadinstitute/sting/utils/AlleleFrequencyEstimate.java b/java/src/org/broadinstitute/sting/playground/utils/AlleleFrequencyEstimate.java
similarity index 92%
rename from playground/java/src/org/broadinstitute/sting/utils/AlleleFrequencyEstimate.java
rename to java/src/org/broadinstitute/sting/playground/utils/AlleleFrequencyEstimate.java
index 5c0dedbc0..87ffda954 100755
--- a/playground/java/src/org/broadinstitute/sting/utils/AlleleFrequencyEstimate.java
+++ b/java/src/org/broadinstitute/sting/playground/utils/AlleleFrequencyEstimate.java
@@ -1,6 +1,6 @@
-package org.broadinstitute.sting.utils;
+package org.broadinstitute.sting.playground.utils;
 
-import org.broadinstitute.sting.gatk.walkers.AlleleFrequencyWalker;
+import org.broadinstitute.sting.playground.gatk.walkers.AlleleFrequencyWalker;
 
 public class AlleleFrequencyEstimate {
     //AlleleFrequencyEstimate();
diff --git a/playground/java/src/org/broadinstitute/sting/utils/CountedObject.java b/java/src/org/broadinstitute/sting/playground/utils/CountedObject.java
similarity index 97%
rename from playground/java/src/org/broadinstitute/sting/utils/CountedObject.java
rename to java/src/org/broadinstitute/sting/playground/utils/CountedObject.java
index d3eb27585..632c4bff5 100755
--- a/playground/java/src/org/broadinstitute/sting/utils/CountedObject.java
+++ b/java/src/org/broadinstitute/sting/playground/utils/CountedObject.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.utils;
+package org.broadinstitute.sting.playground.utils;
 
 /** Utility class that makes working with counted objects slightly easier (and faster). 
  * Consider a "generic" counter representation as Map<Object,Integer>: updating the counter would require
diff --git a/playground/java/src/org/broadinstitute/sting/utils/CountedObjectComparatorAdapter.java b/java/src/org/broadinstitute/sting/playground/utils/CountedObjectComparatorAdapter.java
similarity index 96%
rename from playground/java/src/org/broadinstitute/sting/utils/CountedObjectComparatorAdapter.java
rename to java/src/org/broadinstitute/sting/playground/utils/CountedObjectComparatorAdapter.java
index 80120f083..9d69da144 100755
--- a/playground/java/src/org/broadinstitute/sting/utils/CountedObjectComparatorAdapter.java
+++ b/java/src/org/broadinstitute/sting/playground/utils/CountedObjectComparatorAdapter.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.utils;
+package org.broadinstitute.sting.playground.utils;
 
 
 /** Support class for counted objects. This comparator is an adapter: it is initialized with an arbitrary
diff --git a/playground/java/src/org/broadinstitute/sting/utils/Interval.java b/java/src/org/broadinstitute/sting/playground/utils/Interval.java
similarity index 84%
rename from playground/java/src/org/broadinstitute/sting/utils/Interval.java
rename to java/src/org/broadinstitute/sting/playground/utils/Interval.java
index b5d2cbe96..717f17133 100644
--- a/playground/java/src/org/broadinstitute/sting/utils/Interval.java
+++ b/java/src/org/broadinstitute/sting/playground/utils/Interval.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.utils;
+package org.broadinstitute.sting.playground.utils;
 
 /**
  * Created by IntelliJ IDEA.
@@ -48,12 +48,12 @@ public interface Interval {
       * @param i Another interval
      * @return true iff intervals overlap
      */
-    public boolean overlapsP(org.broadinstitute.sting.utils.Interval i);
+    public boolean overlapsP(org.broadinstitute.sting.playground.utils.Interval i);
 
     /** Returns true if this interval does not overlap with i as judjed by getStart() and getStop() positions of the
      * two interval objects.
       * @param i Another interval
      * @return true iff intervals do not overlap
      */
-    public boolean disjointP(org.broadinstitute.sting.utils.Interval i);
+    public boolean disjointP(org.broadinstitute.sting.playground.utils.Interval i);
 }
diff --git a/playground/java/src/org/broadinstitute/sting/utils/SimpleInterval.java b/java/src/org/broadinstitute/sting/playground/utils/SimpleInterval.java
similarity index 87%
rename from playground/java/src/org/broadinstitute/sting/utils/SimpleInterval.java
rename to java/src/org/broadinstitute/sting/playground/utils/SimpleInterval.java
index d3a1b0519..051672950 100644
--- a/playground/java/src/org/broadinstitute/sting/utils/SimpleInterval.java
+++ b/java/src/org/broadinstitute/sting/playground/utils/SimpleInterval.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.utils;
+package org.broadinstitute.sting.playground.utils;
 
 /**
  * Created by IntelliJ IDEA.
@@ -59,7 +59,7 @@ public class SimpleInterval implements Interval {
      * @return true iff intervals overlap
      */
     @Override
-    public boolean overlapsP(org.broadinstitute.sting.utils.Interval i) {
+    public boolean overlapsP(org.broadinstitute.sting.playground.utils.Interval i) {
         return ! disjointP(i);
     }
 
@@ -69,7 +69,7 @@ public class SimpleInterval implements Interval {
      * @return true iff intervals do not overlap
      */
     @Override
-    public boolean disjointP(org.broadinstitute.sting.utils.Interval i) {
+    public boolean disjointP(org.broadinstitute.sting.playground.utils.Interval i) {
         return ( i.getStop() < this.m_start || i.getStart() > this.m_stop );
     }
 }
diff --git a/playground/java/src/org/broadinstitute/sting/utils/WhitespaceTextFileParser.java b/java/src/org/broadinstitute/sting/playground/utils/WhitespaceTextFileParser.java
similarity index 92%
rename from playground/java/src/org/broadinstitute/sting/utils/WhitespaceTextFileParser.java
rename to java/src/org/broadinstitute/sting/playground/utils/WhitespaceTextFileParser.java
index 5c5bbc8d8..1a5d58140 100644
--- a/playground/java/src/org/broadinstitute/sting/utils/WhitespaceTextFileParser.java
+++ b/java/src/org/broadinstitute/sting/playground/utils/WhitespaceTextFileParser.java
@@ -7,7 +7,7 @@
 * This software is supplied without any warranty or guaranteed support whatsoever. Neither
 * the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
 */
-package org.broadinstitute.sting.utils;
+package org.broadinstitute.sting.playground.utils;
 
 import edu.mit.broad.picard.util.BasicTextFileParser;
 
diff --git a/core/java/src/org/broadinstitute/sting/utils/FastaSequenceFile2.java b/java/src/org/broadinstitute/sting/utils/FastaSequenceFile2.java
similarity index 100%
rename from core/java/src/org/broadinstitute/sting/utils/FastaSequenceFile2.java
rename to java/src/org/broadinstitute/sting/utils/FastaSequenceFile2.java
diff --git a/core/java/src/org/broadinstitute/sting/utils/FileProgressTracker.java b/java/src/org/broadinstitute/sting/utils/FileProgressTracker.java
similarity index 100%
rename from core/java/src/org/broadinstitute/sting/utils/FileProgressTracker.java
rename to java/src/org/broadinstitute/sting/utils/FileProgressTracker.java
diff --git a/core/java/src/org/broadinstitute/sting/utils/GenomeLoc.java b/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
similarity index 100%
rename from core/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
rename to java/src/org/broadinstitute/sting/utils/GenomeLoc.java
diff --git a/core/java/src/org/broadinstitute/sting/utils/Pair.java b/java/src/org/broadinstitute/sting/utils/Pair.java
similarity index 100%
rename from core/java/src/org/broadinstitute/sting/utils/Pair.java
rename to java/src/org/broadinstitute/sting/utils/Pair.java
diff --git a/core/java/src/org/broadinstitute/sting/utils/Predicate.java b/java/src/org/broadinstitute/sting/utils/Predicate.java
similarity index 100%
rename from core/java/src/org/broadinstitute/sting/utils/Predicate.java
rename to java/src/org/broadinstitute/sting/utils/Predicate.java
diff --git a/core/java/src/org/broadinstitute/sting/utils/PrimitivePair.java b/java/src/org/broadinstitute/sting/utils/PrimitivePair.java
similarity index 100%
rename from core/java/src/org/broadinstitute/sting/utils/PrimitivePair.java
rename to java/src/org/broadinstitute/sting/utils/PrimitivePair.java
diff --git a/core/java/src/org/broadinstitute/sting/utils/RefHanger.java b/java/src/org/broadinstitute/sting/utils/RefHanger.java
similarity index 100%
rename from core/java/src/org/broadinstitute/sting/utils/RefHanger.java
rename to java/src/org/broadinstitute/sting/utils/RefHanger.java
diff --git a/core/java/src/org/broadinstitute/sting/utils/Utils.java b/java/src/org/broadinstitute/sting/utils/Utils.java
similarity index 100%
rename from core/java/src/org/broadinstitute/sting/utils/Utils.java
rename to java/src/org/broadinstitute/sting/utils/Utils.java
diff --git a/core/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentParser.java b/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentParser.java
similarity index 100%
rename from core/java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentParser.java
rename to java/src/org/broadinstitute/sting/utils/cmdLine/ArgumentParser.java
diff --git a/core/java/src/org/broadinstitute/sting/utils/cmdLine/CommandLineProgram.java b/java/src/org/broadinstitute/sting/utils/cmdLine/CommandLineProgram.java
similarity index 100%
rename from core/java/src/org/broadinstitute/sting/utils/cmdLine/CommandLineProgram.java
rename to java/src/org/broadinstitute/sting/utils/cmdLine/CommandLineProgram.java