diff --git a/packages/AnalyzeCovariatesModule.xml b/packages/AnalyzeCovariates.xml
similarity index 100%
rename from packages/AnalyzeCovariatesModule.xml
rename to packages/AnalyzeCovariates.xml
diff --git a/packages/FindContaminatingReadGroupsModule.xml b/packages/FindContaminatingReadGroups.xml
similarity index 100%
rename from packages/FindContaminatingReadGroupsModule.xml
rename to packages/FindContaminatingReadGroups.xml
diff --git a/packages/GATK-GSA-Pipeline.xml b/packages/GATK-GSA-Pipeline.xml
index 4d259b64d..155e8d660 100644
--- a/packages/GATK-GSA-Pipeline.xml
+++ b/packages/GATK-GSA-Pipeline.xml
@@ -7,13 +7,13 @@
     <name>GATK-GSA-Pipeline</name>
     <main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
     <properties>StingText.properties</properties>
-    <module>QualityScoresRecalibrationModule.xml</module>
-    <module>LocalRealignmentAroundIndelsModule.xml</module>
-    <module>UnifiedGenotyperModule.xml</module>
-    <module>VariantFiltrationModule.xml</module>
-    <module>VariantAnnotatorModule.xml</module>
-    <module>VariantEvalModule.xml</module>
-    <module>FindContaminatingReadGroupsModule.xml</module>
+    <module>QualityScoresRecalibration.xml</module>
+    <module>LocalRealignmentAroundIndels.xml</module>
+    <module>UnifiedGenotyper.xml</module>
+    <module>VariantFiltration.xml</module>
+    <module>VariantAnnotator.xml</module>
+    <module>VariantEval.xml</module>
+    <module>FindContaminatingReadGroups.xml</module>
     <dependencies>
       <!-- Filters -->
       <package>org.broadinstitute.sting.gatk.filters</package>
diff --git a/packages/GATK-Picard.xml b/packages/GATK-Picard.xml
index 0df3a57f1..1dc8c0877 100644
--- a/packages/GATK-Picard.xml
+++ b/packages/GATK-Picard.xml
@@ -8,11 +8,11 @@
     <name>GATK-Picard</name>
     <main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
     <properties>StingText.properties</properties>
-    <module>QualityScoresRecalibrationModule.xml</module>
-    <module>LocalRealignmentAroundIndelsModule.xml</module>
-    <module>UnifiedGenotyperModule.xml</module>
-    <module>VariantFiltrationModule.xml</module>
-    <module>VariantAnnotatorModule.xml</module>
+    <module>QualityScoresRecalibration.xml</module>
+    <module>LocalRealignmentAroundIndels.xml</module>
+    <module>UnifiedGenotyper.xml</module>
+    <module>VariantFiltration.xml</module>
+    <module>VariantAnnotator.xml</module>
     <dependencies>
       <!-- Filters -->
       <package>org.broadinstitute.sting.gatk.filters</package>
diff --git a/packages/GenomeAnalysisTK.xml b/packages/GenomeAnalysisTK.xml
index 166cc3355..18ff53388 100644
--- a/packages/GenomeAnalysisTK.xml
+++ b/packages/GenomeAnalysisTK.xml
@@ -5,12 +5,12 @@
     <name>GenomeAnalysisTK</name>
     <main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
     <properties>StingText.properties</properties>
-    <module>QualityScoresRecalibrationModule.xml</module>
-    <module>LocalRealignmentAroundIndelsModule.xml</module>
-    <module>UnifiedGenotyperModule.xml</module>
-    <module>VariantFiltrationModule.xml</module>
-    <module>VariantAnnotatorModule.xml</module>
-    <module>VCFValidatorModule.xml</module>
+    <module>QualityScoresRecalibration.xml</module>
+    <module>LocalRealignmentAroundIndels.xml</module>
+    <module>UnifiedGenotyper.xml</module>
+    <module>VariantFiltration.xml</module>
+    <module>VariantAnnotator.xml</module>
+    <module>VCFValidator.xml</module>
     <dependencies>
       <!-- Filters -->
       <package>org.broadinstitute.sting.gatk.filters</package>
diff --git a/packages/LocalRealignmentAroundIndelsModule.xml b/packages/LocalRealignmentAroundIndels.xml
similarity index 100%
rename from packages/LocalRealignmentAroundIndelsModule.xml
rename to packages/LocalRealignmentAroundIndels.xml
diff --git a/packages/QualityScoresRecalibrationModule.xml b/packages/QualityScoresRecalibration.xml
similarity index 100%
rename from packages/QualityScoresRecalibrationModule.xml
rename to packages/QualityScoresRecalibration.xml
diff --git a/packages/UnifiedGenotyperModule.xml b/packages/UnifiedGenotyper.xml
similarity index 100%
rename from packages/UnifiedGenotyperModule.xml
rename to packages/UnifiedGenotyper.xml
diff --git a/packages/VCFValidatorModule.xml b/packages/VCFValidator.xml
similarity index 100%
rename from packages/VCFValidatorModule.xml
rename to packages/VCFValidator.xml
diff --git a/packages/VariantAnnotatorModule.xml b/packages/VariantAnnotator.xml
similarity index 100%
rename from packages/VariantAnnotatorModule.xml
rename to packages/VariantAnnotator.xml
diff --git a/packages/VariantEvalModule.xml b/packages/VariantEval.xml
similarity index 100%
rename from packages/VariantEvalModule.xml
rename to packages/VariantEval.xml
diff --git a/packages/VariantFiltrationModule.xml b/packages/VariantFiltration.xml
similarity index 100%
rename from packages/VariantFiltrationModule.xml
rename to packages/VariantFiltration.xml