diff --git a/public/packages/PicardPrivate.xml b/public/packages/PicardPrivate.xml
index 110b41d3f..581c47979 100644
--- a/public/packages/PicardPrivate.xml
+++ b/public/packages/PicardPrivate.xml
@@ -7,6 +7,8 @@
       <class name="edu.mit.broad.picard.genotype.geli.GeliFileWriter" />
       <class name="edu.mit.broad.picard.genotype.geli.GenotypeLikelihoods" />
       <class name="edu.mit.broad.picard.util.PasteParser" />
+      <class name="edu.mit.broad.picard.util.PicardAggregationFsUtil" />
+      <class name="edu.mit.broad.picard.util.PicardFileSystemUtil" />
       <class name="edu.mit.broad.picard.variation.KnownVariantCodecV2" />
       <class name="edu.mit.broad.picard.variation.KnownVariantCodec" />
       <class name="edu.mit.broad.picard.variation.KnownVariantFileHeader" />
diff --git a/settings/repository/edu.mit.broad/picard-private-parts-1954.jar b/settings/repository/edu.mit.broad/picard-private-parts-1954.jar
deleted file mode 100644
index 67637d3d9..000000000
Binary files a/settings/repository/edu.mit.broad/picard-private-parts-1954.jar and /dev/null differ
diff --git a/settings/repository/edu.mit.broad/picard-private-parts-1954.xml~ b/settings/repository/edu.mit.broad/picard-private-parts-1954.xml~
deleted file mode 100644
index 07d51ae53..000000000
--- a/settings/repository/edu.mit.broad/picard-private-parts-1954.xml~
+++ /dev/null
@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="edu.mit.broad" module="picard-private-parts" revision="1941" status="integration" publication="20110614114100" />
-</ivy-module>
diff --git a/settings/repository/edu.mit.broad/picard-private-parts-1959.jar b/settings/repository/edu.mit.broad/picard-private-parts-1959.jar
new file mode 100644
index 000000000..ae11e636b
Binary files /dev/null and b/settings/repository/edu.mit.broad/picard-private-parts-1959.jar differ
diff --git a/settings/repository/edu.mit.broad/picard-private-parts-1954.xml b/settings/repository/edu.mit.broad/picard-private-parts-1959.xml
similarity index 58%
rename from settings/repository/edu.mit.broad/picard-private-parts-1954.xml
rename to settings/repository/edu.mit.broad/picard-private-parts-1959.xml
index c702fd6e5..e7c7e3a21 100644
--- a/settings/repository/edu.mit.broad/picard-private-parts-1954.xml
+++ b/settings/repository/edu.mit.broad/picard-private-parts-1959.xml
@@ -1,3 +1,3 @@
 <ivy-module version="1.0">
-    <info organisation="edu.mit.broad" module="picard-private-parts" revision="1954" status="integration" publication="20110712113100" />
+    <info organisation="edu.mit.broad" module="picard-private-parts" revision="1959" status="integration" publication="20110718185300" />
 </ivy-module>
diff --git a/settings/repository/net.sf/picard-1.48.889.xml b/settings/repository/net.sf/picard-1.48.889.xml
deleted file mode 100644
index 877687930..000000000
--- a/settings/repository/net.sf/picard-1.48.889.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf" module="picard" revision="1.48.889" status="release" />
-</ivy-module>
diff --git a/settings/repository/net.sf/picard-1.48.889.jar b/settings/repository/net.sf/picard-1.49.895.jar
similarity index 95%
rename from settings/repository/net.sf/picard-1.48.889.jar
rename to settings/repository/net.sf/picard-1.49.895.jar
index 1b725dde5..3ee1f2090 100644
Binary files a/settings/repository/net.sf/picard-1.48.889.jar and b/settings/repository/net.sf/picard-1.49.895.jar differ
diff --git a/settings/repository/net.sf/picard-1.49.895.xml b/settings/repository/net.sf/picard-1.49.895.xml
new file mode 100644
index 000000000..52d4900c5
--- /dev/null
+++ b/settings/repository/net.sf/picard-1.49.895.xml
@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf" module="picard" revision="1.49.895" status="release" />
+</ivy-module>
diff --git a/settings/repository/net.sf/sam-1.48.889.xml b/settings/repository/net.sf/sam-1.48.889.xml
deleted file mode 100644
index 8046a0c02..000000000
--- a/settings/repository/net.sf/sam-1.48.889.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf" module="sam" revision="1.48.889" status="release" />
-</ivy-module>
diff --git a/settings/repository/net.sf/sam-1.48.889.jar b/settings/repository/net.sf/sam-1.49.895.jar
similarity index 95%
rename from settings/repository/net.sf/sam-1.48.889.jar
rename to settings/repository/net.sf/sam-1.49.895.jar
index 33ae4aa7d..c55ab0b72 100644
Binary files a/settings/repository/net.sf/sam-1.48.889.jar and b/settings/repository/net.sf/sam-1.49.895.jar differ
diff --git a/settings/repository/net.sf/sam-1.49.895.xml b/settings/repository/net.sf/sam-1.49.895.xml
new file mode 100644
index 000000000..0436ce881
--- /dev/null
+++ b/settings/repository/net.sf/sam-1.49.895.xml
@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf" module="sam" revision="1.49.895" status="release" />
+</ivy-module>