diff --git a/java/src/org/broadinstitute/sting/gatk/examples/papergenotyper/package-info.java b/java/src/org/broadinstitute/sting/gatk/examples/papergenotyper/package-info.java
index f3d262f99..976e4b469 100644
--- a/java/src/org/broadinstitute/sting/gatk/examples/papergenotyper/package-info.java
+++ b/java/src/org/broadinstitute/sting/gatk/examples/papergenotyper/package-info.java
@@ -1,4 +1,4 @@
 /**
  * @help.display.name The GATK paper's Bayesian genotyper
  */
-package org.broadinstitute.sting.playground.gatk.walkers.papergenotyper;
\ No newline at end of file
+package org.broadinstitute.sting.gatk.examples.papergenotyper;
diff --git a/packages/GenomeAnalysisTK.xml b/packages/GenomeAnalysisTK.xml
index 68acccfaa..fb2d36873 100644
--- a/packages/GenomeAnalysisTK.xml
+++ b/packages/GenomeAnalysisTK.xml
@@ -4,33 +4,15 @@
   <executable name="GenomeAnalysisTK">
     <main-class name="org.broadinstitute.sting.gatk.CommandLineGATK" />
     <resource-bundle file="StingText.properties" />
-    <modules>
-      <module file="QualityScoresRecalibration.xml" />
-      <module file="VariantRecalibration.xml" />
-      <module file="LocalRealignmentAroundIndels.xml" />
-      <module file="UnifiedGenotyper.xml" />
-      <module file="VariantEval.xml" />
-      <module file="VariantFiltration.xml" />
-      <module file="VariantAnnotator.xml" />
-      <module file="IndelGenotyper.xml" />
-    </modules>
     <dependencies>
+      <!-- Core walkers -->
+      <package name="org.broadinstitute.sting.gatk.walkers.**" />
       <!-- Filters -->
       <package name="org.broadinstitute.sting.gatk.filters" />
       <!-- Tribble codecs -->
       <package name="org.broad.tribble.*" />
-      <!-- Basic qc walkers -->
-      <class name="org.broadinstitute.sting.gatk.walkers.coverage.DepthOfCoverageWalker" />
-      <class name="org.broadinstitute.sting.gatk.walkers.coverage.DoCOutputMultiplexer" />
-
-      <class name="org.broadinstitute.sting.gatk.walkers.PileupWalker" />
-      <class name="org.broadinstitute.sting.gatk.walkers.PrintReadsWalker" />
-      <class name="org.broadinstitute.sting.gatk.walkers.qc.CountLociWalker" />
-      <class name="org.broadinstitute.sting.gatk.walkers.qc.CountReadsWalker" />
-      <class name="org.broadinstitute.sting.gatk.walkers.qc.ValidatingPileupWalker" />
-      <!-- Other misc walkers -->
-      <class name="org.broadinstitute.sting.gatk.walkers.variantutils.CombineVariants" />
-      <class name="org.broadinstitute.sting.gatk.walkers.VariantsToVCF" />
+      <!-- Workaround - depend on the logger impl required by JEXL -->
+      <package name="org.apache.commons.logging.impl" />
     </dependencies>
   </executable>
   <modules>
diff --git a/perl/runReleaseSanityCheck.pl b/perl/runReleaseSanityCheck.pl
index c237cbf4f..2d62b5dc6 100755
--- a/perl/runReleaseSanityCheck.pl
+++ b/perl/runReleaseSanityCheck.pl
@@ -19,11 +19,11 @@ $command = "$command_prefix -T DepthOfCoverage -I /humgen/gsa-hpprojects/GATK/da
 run($command, $dry);
 
 print "Executing CountCovariatesWholeExome...";
-$command = "$command_prefix -T CountCovariates -I /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.ESP.WEx.chr1.bam -L /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/whole_exome_agilent_designed_120.targets.chr1.interval_list -standard -OQ -recalFile /dev/null -XL chr1:1,000,000-247179187";
+$command = "$command_prefix -T CountCovariates -I /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.ESP.WEx.chr1.bam -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod -L /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/whole_exome_agilent_designed_120.targets.chr1.interval_list -standard -OQ -recalFile /dev/null -XL chr1:1,000,000-247179187";
 run($command, $dry);
 
 print "Executing CountCovariatesWholeGenome...";
-$command = "$command_prefix -T CountCovariates -I /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.GAII.chr1.50MB.bam -L chr1:1,900,000-2,000,000 -standard -OQ -recalFile /dev/null";
+$command = "$command_prefix -T CountCovariates -I /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.GAII.chr1.50MB.bam -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod -L chr1:1,900,000-2,000,000 -standard -OQ -recalFile /dev/null";
 run($command, $dry);
 
 print "Executing TableRecalibratorWholeExome...";