Merged bug fix from Stable into Unstable

Conflicts:
	private/java/src/org/broadinstitute/sting/pipeline/ReferenceData.java

settings/repository/edu.mit.broad/picard-private-parts-2034.xml

@@ -1,3 +1,3 @@
 <ivy-module version="1.0">
-    <info organisation="edu.mit.broad" module="picard-private-parts" revision="1959" status="integration" publication="20110718185300" />
+    <info organisation="edu.mit.broad" module="picard-private-parts" revision="2034" status="integration" publication="20110718185300" />
 </ivy-module>

settings/repository/net.sf/picard-1.49.895.xml

@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf" module="picard" revision="1.49.895" status="release" />
-</ivy-module>

settings/repository/net.sf/picard-1.52.944.xml

@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf" module="picard" revision="1.52.944" status="release" />
+</ivy-module>

settings/repository/net.sf/sam-1.49.895.xml

@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf" module="sam" revision="1.49.895" status="release" />
-</ivy-module>

settings/repository/net.sf/sam-1.52.944.xml

@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf" module="sam" revision="1.52.944" status="release" />
+</ivy-module>