diff --git a/packages/Aligner.xml b/packages/Aligner.xml
index 039daa57c..cdb154648 100644
--- a/packages/Aligner.xml
+++ b/packages/Aligner.xml
@@ -1,8 +1,11 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <package>
   <name>Aligner</name>
-  <dependencies>
-    <!-- BWA/C aligner implementation -->
-    <class>org.broadinstitute.sting.alignment.bwa.c.BWACAligner</class>
-  </dependencies>
+  <executable>
+    <name>Aligner</name>
+    <dependencies>
+      <!-- BWA/C aligner implementation -->
+      <class>org.broadinstitute.sting.alignment.bwa.c.BWACAligner</class>
+    </dependencies>
+  </executable>
 </package>
diff --git a/packages/AnalyzeCovariates.xml b/packages/AnalyzeCovariates.xml
deleted file mode 100644
index 9fdfb1d37..000000000
--- a/packages/AnalyzeCovariates.xml
+++ /dev/null
@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<package>
-  <name>AnalyzeCovariates</name>
-  <main-class>org.broadinstitute.sting.analyzecovariates.AnalyzeCovariates</main-class>
-  <dependencies>
-    <!-- Recalibration analysis script -->
-    <class>org.broadinstitute.sting.analyzecovariates.AnalyzeCovariates</class>
-    <class>org.broadinstitute.sting.gatk.walkers.recalibration.DinucCovariate</class>
-    <class>org.broadinstitute.sting.gatk.walkers.recalibration.PositionCovariate</class>
-    <class>org.broadinstitute.sting.gatk.walkers.recalibration.MinimumNQSCovariate</class>
-    <class>org.broadinstitute.sting.gatk.walkers.recalibration.MappingQualityCovariate</class>
-    <class>org.broadinstitute.sting.gatk.walkers.recalibration.QualityScoreCovariate</class>
-    <class>org.broadinstitute.sting.gatk.walkers.recalibration.PrimerRoundCovariate</class>
-    <class>org.broadinstitute.sting.gatk.walkers.recalibration.CycleCovariate</class>
-    <class>org.broadinstitute.sting.gatk.walkers.recalibration.ReadGroupCovariate</class>
-  </dependencies>
-</package>
diff --git a/packages/AnnotateSecondaryBase.xml b/packages/AnnotateSecondaryBase.xml
deleted file mode 100644
index 766310f20..000000000
--- a/packages/AnnotateSecondaryBase.xml
+++ /dev/null
@@ -1,5 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<package>
-  <name>AnnotateSecondaryBase</name>
-  <main-class>org.broadinstitute.sting.secondarybase.AnnotateSecondaryBase</main-class>
-</package>
diff --git a/packages/CreatePackager.xsl b/packages/CreatePackager.xsl
index 00545ba9e..7b1233007 100644
--- a/packages/CreatePackager.xsl
+++ b/packages/CreatePackager.xsl
@@ -20,7 +20,7 @@
 
     <target name="package">
       <!-- Verify that all classes specified are present -->
-      <xsl:for-each select="dependencies/class">
+      <xsl:for-each select="//class">
 	<available property="is.{current()}.present" classpath="{$classpath}" classname="{current()}"/>
 	<fail message="Class {current()} not found" unless="is.{current()}.present" />
       </xsl:for-each>
@@ -28,24 +28,26 @@
       <!-- Create an output directory for the package -->
       <mkdir dir="{$package.dir}"/>
 
-      <!-- Create a jar file containing the specified classes / packages and all their dependencies -->
-      <jar jarfile="{concat($package.dir,$project.name,'.jar')}">
-        <classfileset dir="{$staging.dir}">
-          <root classname="{main-class}"/>
-          <xsl:for-each select="dependencies/package">
-            <rootfileset dir="{$staging.dir}" includes="{concat(translate(current(),'.','/'),'/','*.class')}" />
+      <xsl:for-each select="executable">
+	<!-- Create a jar file containing the specified classes / packages and all their dependencies -->
+	<jar jarfile="{concat($package.dir,name,'.jar')}">
+          <classfileset dir="{$staging.dir}">
+            <root classname="{main-class}"/>
+            <xsl:for-each select="dependencies/package">
+              <rootfileset dir="{$staging.dir}" includes="{concat(translate(current(),'.','/'),'/','*.class')}" />
+            </xsl:for-each>
+            <xsl:for-each select="dependencies/class">
+              <root classname="{current()}" />
+            </xsl:for-each>
+          </classfileset>
+          <xsl:for-each select="dependencies/file">
+            <fileset file="{current()}" />
           </xsl:for-each>
-          <xsl:for-each select="dependencies/class">
-            <root classname="{current()}" />
-          </xsl:for-each>
-        </classfileset>
-        <xsl:for-each select="dependencies/file">
-          <fileset file="{current()}" />
-        </xsl:for-each>
-        <manifest>
-          <attribute name="Main-Class" value="{main-class}"/>
-        </manifest>
-      </jar>
+          <manifest>
+            <attribute name="Main-Class" value="{main-class}"/>
+          </manifest>
+	</jar>
+      </xsl:for-each>
 
       <!-- Include various script files -->
       <xsl:for-each select="scripts/file">
diff --git a/packages/GenomeAnalysisTK.xml b/packages/GenomeAnalysisTK.xml
index 51814abcd..860c8b54c 100644
--- a/packages/GenomeAnalysisTK.xml
+++ b/packages/GenomeAnalysisTK.xml
@@ -1,50 +1,69 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <package>
   <name>GenomeAnalysisTK</name>
-  <main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
-  <dependencies>
-    <package>org.broadinstitute.sting.gatk.filters</package>
-    <class>org.broadinstitute.sting.gatk.walkers.CountLociWalker</class>
-    <class>org.broadinstitute.sting.gatk.walkers.CountReadsWalker</class>
-    <class>org.broadinstitute.sting.gatk.walkers.DepthOfCoverageWalker</class>
-    <class>org.broadinstitute.sting.gatk.walkers.PileupWalker</class>
-    <class>org.broadinstitute.sting.gatk.walkers.PrintReadsWalker</class>
-    <class>org.broadinstitute.sting.gatk.walkers.ValidatingPileupWalker</class>
-    <!-- Quality scores recalibration -->
-    <class>org.broadinstitute.sting.gatk.walkers.recalibration.CovariateCounterWalker</class>
-    <class>org.broadinstitute.sting.gatk.walkers.recalibration.TableRecalibrationWalker</class>
-    <!-- Recalibration Covariates -->
-    <class>org.broadinstitute.sting.gatk.walkers.recalibration.DinucCovariate</class>
-    <class>org.broadinstitute.sting.gatk.walkers.recalibration.PositionCovariate</class>
-    <class>org.broadinstitute.sting.gatk.walkers.recalibration.MinimumNQSCovariate</class>
-    <class>org.broadinstitute.sting.gatk.walkers.recalibration.MappingQualityCovariate</class>
-    <class>org.broadinstitute.sting.gatk.walkers.recalibration.QualityScoreCovariate</class>
-    <class>org.broadinstitute.sting.gatk.walkers.recalibration.PrimerRoundCovariate</class>
-    <class>org.broadinstitute.sting.gatk.walkers.recalibration.CycleCovariate</class>
-    <class>org.broadinstitute.sting.gatk.walkers.recalibration.ReadGroupCovariate</class>
-    <!-- Local realignment around indels -->
-    <class>org.broadinstitute.sting.gatk.walkers.indels.CleanedReadInjector</class>
-    <class>org.broadinstitute.sting.gatk.walkers.indels.IndelIntervalWalker</class>
-    <class>org.broadinstitute.sting.gatk.walkers.indels.IntervalCleanerWalker</class>
-    <class>org.broadinstitute.sting.gatk.walkers.indels.IntervalMergerWalker</class>
-    <class>org.broadinstitute.sting.gatk.walkers.indels.MismatchIntervalWalker</class>
-    <class>org.broadinstitute.sting.gatk.walkers.indels.SNPClusterWalker</class>
-    <class>org.broadinstitute.sting.gatk.walkers.indels.IndelGenotyperWalker</class>
-    <class>org.broadinstitute.sting.gatk.walkers.indels.IndelGenotyperV2Walker</class> 
-    <!-- Unified genotyper -->
-    <class>org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper</class>
-    <!-- Variant filtration -->
-    <class>org.broadinstitute.sting.gatk.walkers.filters.VariantFiltrationWalker</class>
-    <!-- Variant annotator -->
-    <class>org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotator</class>
-    <!-- And the annotations -->
-    <class>org.broadinstitute.sting.gatk.walkers.annotator.AlleleBalance</class>
-    <class>org.broadinstitute.sting.gatk.walkers.annotator.DepthOfCoverage</class>
-    <class>org.broadinstitute.sting.gatk.walkers.annotator.HomopolymerRun</class>
-    <class>org.broadinstitute.sting.gatk.walkers.annotator.MappingQualityZero</class>
-    <class>org.broadinstitute.sting.gatk.walkers.annotator.RMSMappingQuality</class>
-    <class>org.broadinstitute.sting.gatk.walkers.annotator.SpanningDeletions</class>
-  </dependencies>
+  <executable>
+    <name>GenomeAnalysisTK</name>
+    <main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
+    <dependencies>
+      <package>org.broadinstitute.sting.gatk.filters</package>
+      <class>org.broadinstitute.sting.gatk.walkers.CountLociWalker</class>
+      <class>org.broadinstitute.sting.gatk.walkers.CountReadsWalker</class>
+      <class>org.broadinstitute.sting.gatk.walkers.DepthOfCoverageWalker</class>
+      <class>org.broadinstitute.sting.gatk.walkers.PileupWalker</class>
+      <class>org.broadinstitute.sting.gatk.walkers.PrintReadsWalker</class>
+      <class>org.broadinstitute.sting.gatk.walkers.qc.ValidatingPileupWalker</class>
+      <!-- Quality scores recalibration -->
+      <class>org.broadinstitute.sting.gatk.walkers.recalibration.CovariateCounterWalker</class>
+      <class>org.broadinstitute.sting.gatk.walkers.recalibration.TableRecalibrationWalker</class>
+      <!-- Recalibration Covariates -->
+      <class>org.broadinstitute.sting.gatk.walkers.recalibration.DinucCovariate</class>
+      <class>org.broadinstitute.sting.gatk.walkers.recalibration.PositionCovariate</class>
+      <class>org.broadinstitute.sting.gatk.walkers.recalibration.MinimumNQSCovariate</class>
+      <class>org.broadinstitute.sting.gatk.walkers.recalibration.MappingQualityCovariate</class>
+      <class>org.broadinstitute.sting.gatk.walkers.recalibration.QualityScoreCovariate</class>
+      <class>org.broadinstitute.sting.gatk.walkers.recalibration.PrimerRoundCovariate</class>
+      <class>org.broadinstitute.sting.gatk.walkers.recalibration.CycleCovariate</class>
+      <class>org.broadinstitute.sting.gatk.walkers.recalibration.ReadGroupCovariate</class>
+      <!-- Local realignment around indels -->
+      <class>org.broadinstitute.sting.gatk.walkers.indels.CleanedReadInjector</class>
+      <class>org.broadinstitute.sting.gatk.walkers.indels.IndelIntervalWalker</class>
+      <class>org.broadinstitute.sting.gatk.walkers.indels.IntervalCleanerWalker</class>
+      <class>org.broadinstitute.sting.gatk.walkers.indels.IntervalMergerWalker</class>
+      <class>org.broadinstitute.sting.gatk.walkers.indels.MismatchIntervalWalker</class>
+      <class>org.broadinstitute.sting.gatk.walkers.indels.SNPClusterWalker</class>
+      <class>org.broadinstitute.sting.gatk.walkers.indels.IndelGenotyperWalker</class>
+      <class>org.broadinstitute.sting.gatk.walkers.indels.IndelGenotyperV2Walker</class> 
+      <!-- Unified genotyper -->
+      <class>org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper</class>
+      <!-- Variant filtration -->
+      <class>org.broadinstitute.sting.gatk.walkers.filters.VariantFiltrationWalker</class>
+      <!-- Variant annotator -->
+      <class>org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotator</class>
+      <!-- And the annotations -->
+      <class>org.broadinstitute.sting.gatk.walkers.annotator.AlleleBalance</class>
+      <class>org.broadinstitute.sting.gatk.walkers.annotator.DepthOfCoverage</class>
+      <class>org.broadinstitute.sting.gatk.walkers.annotator.HomopolymerRun</class>
+      <class>org.broadinstitute.sting.gatk.walkers.annotator.MappingQualityZero</class>
+      <class>org.broadinstitute.sting.gatk.walkers.annotator.RMSMappingQuality</class>
+      <class>org.broadinstitute.sting.gatk.walkers.annotator.SpanningDeletions</class>
+    </dependencies>
+  </executable>
+  <executable>
+    <name>AnalyzeCovariates</name>
+    <main-class>org.broadinstitute.sting.analyzecovariates.AnalyzeCovariates</main-class>
+    <dependencies>
+      <!-- Recalibration analysis script -->
+      <class>org.broadinstitute.sting.analyzecovariates.AnalyzeCovariates</class>
+      <class>org.broadinstitute.sting.gatk.walkers.recalibration.DinucCovariate</class>
+      <class>org.broadinstitute.sting.gatk.walkers.recalibration.PositionCovariate</class>
+      <class>org.broadinstitute.sting.gatk.walkers.recalibration.MinimumNQSCovariate</class>
+      <class>org.broadinstitute.sting.gatk.walkers.recalibration.MappingQualityCovariate</class>
+      <class>org.broadinstitute.sting.gatk.walkers.recalibration.QualityScoreCovariate</class>
+      <class>org.broadinstitute.sting.gatk.walkers.recalibration.PrimerRoundCovariate</class>
+      <class>org.broadinstitute.sting.gatk.walkers.recalibration.CycleCovariate</class>
+      <class>org.broadinstitute.sting.gatk.walkers.recalibration.ReadGroupCovariate</class>
+    </dependencies>
+  </executable>
   <resources>
     <!-- GATK sample code and build scripts -->
     <file>java/src/org/broadinstitute/sting/gatk/walkers/CountReadsWalker.java</file>
@@ -52,7 +71,7 @@
     <file>java/src/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageWalker.java</file>
     <file>java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java</file>
     <file>java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java</file>
-    <file>java/src/org/broadinstitute/sting/gatk/walkers/ValidatingPileupWalker.java</file>
+    <file>java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java</file>
     <file>java/src/org/broadinstitute/sting/gatk/examples/HelloWalker.java</file>
     <file>java/src/org/broadinstitute/sting/gatk/examples/build.xml</file>
     <!-- Sample reads and reference files -->
diff --git a/packages/PicardPrivate.xml b/packages/PicardPrivate.xml
index 02f1549e0..6a424cc6d 100644
--- a/packages/PicardPrivate.xml
+++ b/packages/PicardPrivate.xml
@@ -1,29 +1,32 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <package>
   <name>picard-private-parts</name>
-  <dependencies>
-    <class>edu.mit.broad.picard.directed.IntervalList</class>
-    <class>edu.mit.broad.picard.genotype.DiploidGenotype</class>
-    <class>edu.mit.broad.picard.genotype.geli.GeliFileReader</class>
-    <class>edu.mit.broad.picard.genotype.geli.GeliFileWriter</class>
-    <class>edu.mit.broad.picard.genotype.geli.GenotypeLikelihoods</class>
-    <class>edu.mit.broad.picard.util.BasicTextFileParser</class>
-    <class>edu.mit.broad.picard.illumina.parser.IlluminaUtil</class>
-    <class>edu.mit.broad.picard.util.Interval</class>
-    <class>edu.mit.broad.picard.util.IntervalTree</class>
-    <class>edu.mit.broad.picard.util.OverlapDetector</class>
-    <class>edu.mit.broad.picard.util.PasteParser</class>
-    <class>edu.mit.broad.picard.variation.KnownVariantCodecV2</class>
-    <class>edu.mit.broad.picard.variation.KnownVariantCodec</class>
-    <class>edu.mit.broad.picard.variation.KnownVariantFileHeader</class>
-    <class>edu.mit.broad.picard.variation.GenerateDbSnpFile</class>
-    <class>edu.mit.broad.picard.variation.VariantType</class>
-    <class>edu.mit.broad.picard.variation.ObsoleteKnownVariantCodecV1</class>
-    <class>edu.mit.broad.picard.variation.AbstractKnownVariantCodec</class>
-    <class>edu.mit.broad.picard.variation.KnownVariantIterator</class>
-    <class>edu.mit.broad.picard.variation.KnownVariantCodecFactory</class>
-    <class>edu.mit.broad.picard.variation.KnownVariant</class>
-    <class>edu.mit.broad.picard.variation.DbSnpFileReader</class>
-    <class>edu.mit.broad.picard.variation.DbSnpFileGenerator</class>
-  </dependencies>
+  <executable>
+    <name>picard-private-parts</name>
+    <dependencies>
+      <class>edu.mit.broad.picard.directed.IntervalList</class>
+      <class>edu.mit.broad.picard.genotype.DiploidGenotype</class>
+      <class>edu.mit.broad.picard.genotype.geli.GeliFileReader</class>
+      <class>edu.mit.broad.picard.genotype.geli.GeliFileWriter</class>
+      <class>edu.mit.broad.picard.genotype.geli.GenotypeLikelihoods</class>
+      <class>edu.mit.broad.picard.util.BasicTextFileParser</class>
+      <class>edu.mit.broad.picard.illumina.parser.IlluminaUtil</class>
+      <class>edu.mit.broad.picard.util.Interval</class>
+      <class>edu.mit.broad.picard.util.IntervalTree</class>
+      <class>edu.mit.broad.picard.util.OverlapDetector</class>
+      <class>edu.mit.broad.picard.util.PasteParser</class>
+      <class>edu.mit.broad.picard.variation.KnownVariantCodecV2</class>
+      <class>edu.mit.broad.picard.variation.KnownVariantCodec</class>
+      <class>edu.mit.broad.picard.variation.KnownVariantFileHeader</class>
+      <class>edu.mit.broad.picard.variation.GenerateDbSnpFile</class>
+      <class>edu.mit.broad.picard.variation.VariantType</class>
+      <class>edu.mit.broad.picard.variation.ObsoleteKnownVariantCodecV1</class>
+      <class>edu.mit.broad.picard.variation.AbstractKnownVariantCodec</class>
+      <class>edu.mit.broad.picard.variation.KnownVariantIterator</class>
+      <class>edu.mit.broad.picard.variation.KnownVariantCodecFactory</class>
+      <class>edu.mit.broad.picard.variation.KnownVariant</class>
+      <class>edu.mit.broad.picard.variation.DbSnpFileReader</class>
+      <class>edu.mit.broad.picard.variation.DbSnpFileGenerator</class>
+    </dependencies>
+  </executable>
 </package>
diff --git a/packages/SomaticCoverage.xml b/packages/SomaticCoverage.xml
deleted file mode 100644
index f0520c611..000000000
--- a/packages/SomaticCoverage.xml
+++ /dev/null
@@ -1,9 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<package>
-  <name>SomaticCoverage</name>
-  <main-class>org.broadinstitute.sting.playground.somaticcoverage.SomaticCoverageTool</main-class>
-  <dependencies>
-    <class>org.broadinstitute.sting.playground.gatk.walkers.SomaticCoverageWalker</class>
-    <file>java/src/org/broadinstitute/sting/playground/somaticcoverage/SomaticCoverage.xml</file>
-  </dependencies>
-</package>
diff --git a/packages/VCFValidator.xml b/packages/VCFValidator.xml
index b6abd4f23..e47944d4d 100644
--- a/packages/VCFValidator.xml
+++ b/packages/VCFValidator.xml
@@ -1,5 +1,8 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <package>
   <name>VCFValidator</name>
-  <main-class>org.broadinstitute.sting.utils.genotype.vcf.VCFValidator</main-class>
+  <executable>
+    <name>VCFValidator</name>
+    <main-class>org.broadinstitute.sting.utils.genotype.vcf.VCFValidator</main-class>
+  </executable>
 </package>