diff --git a/settings/repository/com.google.code.caliper/caliper-1.0-SNAPSHOT.jar b/public/repo/com/google/code/caliper/caliper/1.0-SNAPSHOT/caliper-1.0-SNAPSHOT.jar
similarity index 100%
rename from settings/repository/com.google.code.caliper/caliper-1.0-SNAPSHOT.jar
rename to public/repo/com/google/code/caliper/caliper/1.0-SNAPSHOT/caliper-1.0-SNAPSHOT.jar
diff --git a/public/repo/com/google/code/caliper/caliper/1.0-SNAPSHOT/caliper-1.0-SNAPSHOT.pom b/public/repo/com/google/code/caliper/caliper/1.0-SNAPSHOT/caliper-1.0-SNAPSHOT.pom
new file mode 100644
index 000000000..683ac1ae3
--- /dev/null
+++ b/public/repo/com/google/code/caliper/caliper/1.0-SNAPSHOT/caliper-1.0-SNAPSHOT.pom
@@ -0,0 +1,9 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+  <modelVersion>4.0.0</modelVersion>
+  <groupId>com.google.code.caliper</groupId>
+  <artifactId>caliper</artifactId>
+  <name>caliper</name>
+  <version>1.0-SNAPSHOT</version>
+</project>
diff --git a/settings/repository/com.google.code.cofoja/cofoja-1.0-r139.jar b/public/repo/com/google/code/cofoja/cofoja/1.0-r139/cofoja-1.0-r139.jar
similarity index 100%
rename from settings/repository/com.google.code.cofoja/cofoja-1.0-r139.jar
rename to public/repo/com/google/code/cofoja/cofoja/1.0-r139/cofoja-1.0-r139.jar
diff --git a/public/repo/com/google/code/cofoja/cofoja/1.0-r139/cofoja-1.0-r139.pom b/public/repo/com/google/code/cofoja/cofoja/1.0-r139/cofoja-1.0-r139.pom
new file mode 100644
index 000000000..5a6fb69b9
--- /dev/null
+++ b/public/repo/com/google/code/cofoja/cofoja/1.0-r139/cofoja-1.0-r139.pom
@@ -0,0 +1,9 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+  <modelVersion>4.0.0</modelVersion>
+  <groupId>com.google.code.cofoja</groupId>
+  <artifactId>cofoja</artifactId>
+  <name>cofoja</name>
+  <version>1.0-r139</version>
+</project>
diff --git a/settings/repository/gov.nist/Jama-1.0.2.jar b/public/repo/gov/nist/Jama/1.0.2/Jama-1.0.2.jar
similarity index 100%
rename from settings/repository/gov.nist/Jama-1.0.2.jar
rename to public/repo/gov/nist/Jama/1.0.2/Jama-1.0.2.jar
diff --git a/public/repo/gov/nist/Jama/1.0.2/Jama-1.0.2.pom b/public/repo/gov/nist/Jama/1.0.2/Jama-1.0.2.pom
new file mode 100644
index 000000000..33d13d1ab
--- /dev/null
+++ b/public/repo/gov/nist/Jama/1.0.2/Jama-1.0.2.pom
@@ -0,0 +1,9 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+  <modelVersion>4.0.0</modelVersion>
+  <groupId>gov.nist</groupId>
+  <artifactId>Jama</artifactId>
+  <name>Jama</name>
+  <version>1.0.2</version>
+</project>
diff --git a/settings/repository/net.sf.gridscheduler/drmaa-6.2u5p2.jar b/public/repo/net/sf/gridscheduler/drmaa/6.2u5p2/drmaa-6.2u5p2.jar
similarity index 100%
rename from settings/repository/net.sf.gridscheduler/drmaa-6.2u5p2.jar
rename to public/repo/net/sf/gridscheduler/drmaa/6.2u5p2/drmaa-6.2u5p2.jar
diff --git a/public/repo/net/sf/gridscheduler/drmaa/6.2u5p2/drmaa-6.2u5p2.pom b/public/repo/net/sf/gridscheduler/drmaa/6.2u5p2/drmaa-6.2u5p2.pom
new file mode 100644
index 000000000..921635c84
--- /dev/null
+++ b/public/repo/net/sf/gridscheduler/drmaa/6.2u5p2/drmaa-6.2u5p2.pom
@@ -0,0 +1,9 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+  <modelVersion>4.0.0</modelVersion>
+  <groupId>net.sf.gridscheduler</groupId>
+  <artifactId>drmaa</artifactId>
+  <name>drmaa</name>
+  <version>6.2u5p2</version>
+</project>
diff --git a/settings/repository/net.sf/picard-1.104.1628.jar b/public/repo/net/sf/picard/1.104.1628/picard-1.104.1628.jar
similarity index 100%
rename from settings/repository/net.sf/picard-1.104.1628.jar
rename to public/repo/net/sf/picard/1.104.1628/picard-1.104.1628.jar
diff --git a/public/repo/net/sf/picard/1.104.1628/picard-1.104.1628.pom b/public/repo/net/sf/picard/1.104.1628/picard-1.104.1628.pom
new file mode 100644
index 000000000..c2f2a5048
--- /dev/null
+++ b/public/repo/net/sf/picard/1.104.1628/picard-1.104.1628.pom
@@ -0,0 +1,9 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+  <modelVersion>4.0.0</modelVersion>
+  <groupId>net.sf.snpeff</groupId>
+  <artifactId>picard</artifactId>
+  <name>picard</name>
+  <version>1.104.1628</version>
+</project>
diff --git a/settings/repository/net.sf/sam-1.104.1628.jar b/public/repo/net/sf/sam/1.104.1628/sam-1.104.1628.jar
similarity index 100%
rename from settings/repository/net.sf/sam-1.104.1628.jar
rename to public/repo/net/sf/sam/1.104.1628/sam-1.104.1628.jar
diff --git a/public/repo/net/sf/sam/1.104.1628/sam-1.104.1628.pom b/public/repo/net/sf/sam/1.104.1628/sam-1.104.1628.pom
new file mode 100644
index 000000000..4d9e63822
--- /dev/null
+++ b/public/repo/net/sf/sam/1.104.1628/sam-1.104.1628.pom
@@ -0,0 +1,9 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+  <modelVersion>4.0.0</modelVersion>
+  <groupId>net.sf</groupId>
+  <artifactId>sam</artifactId>
+  <name>sam</name>
+  <version>1.104.1628</version>
+</project>
diff --git a/settings/repository/net.sf.snpeff/snpeff-2.0.5.jar b/public/repo/net/sf/snpeff/snpeff/2.0.5/snpeff-2.0.5.jar
similarity index 100%
rename from settings/repository/net.sf.snpeff/snpeff-2.0.5.jar
rename to public/repo/net/sf/snpeff/snpeff/2.0.5/snpeff-2.0.5.jar
diff --git a/public/repo/net/sf/snpeff/snpeff/2.0.5/snpeff-2.0.5.pom b/public/repo/net/sf/snpeff/snpeff/2.0.5/snpeff-2.0.5.pom
new file mode 100644
index 000000000..d316e2055
--- /dev/null
+++ b/public/repo/net/sf/snpeff/snpeff/2.0.5/snpeff-2.0.5.pom
@@ -0,0 +1,9 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+  <modelVersion>4.0.0</modelVersion>
+  <groupId>net.sf</groupId>
+  <artifactId>snpeff</artifactId>
+  <name>snpeff</name>
+  <version>2.0.5</version>
+</project>
diff --git a/settings/repository/org.broad/tribble-1.104.1628.jar b/public/repo/org/broad/tribble/1.104.1628/tribble-1.104.1628.jar
similarity index 100%
rename from settings/repository/org.broad/tribble-1.104.1628.jar
rename to public/repo/org/broad/tribble/1.104.1628/tribble-1.104.1628.jar
diff --git a/public/repo/org/broad/tribble/1.104.1628/tribble-1.104.1628.pom b/public/repo/org/broad/tribble/1.104.1628/tribble-1.104.1628.pom
new file mode 100644
index 000000000..9acaf0dd1
--- /dev/null
+++ b/public/repo/org/broad/tribble/1.104.1628/tribble-1.104.1628.pom
@@ -0,0 +1,9 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+  <modelVersion>4.0.0</modelVersion>
+  <groupId>org.broad</groupId>
+  <artifactId>tribble</artifactId>
+  <name>tribble</name>
+  <version>1.104.1628</version>
+</project>
diff --git a/settings/repository/org.broadinstitute/variant-1.105.1642.jar b/public/repo/org/broadinstitute/variant/1.105.1642/variant-1.105.1642.jar
similarity index 100%
rename from settings/repository/org.broadinstitute/variant-1.105.1642.jar
rename to public/repo/org/broadinstitute/variant/1.105.1642/variant-1.105.1642.jar
diff --git a/public/repo/org/broadinstitute/variant/1.105.1642/variant-1.105.1642.pom b/public/repo/org/broadinstitute/variant/1.105.1642/variant-1.105.1642.pom
new file mode 100644
index 000000000..7fafe61f4
--- /dev/null
+++ b/public/repo/org/broadinstitute/variant/1.105.1642/variant-1.105.1642.pom
@@ -0,0 +1,9 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+  <modelVersion>4.0.0</modelVersion>
+  <groupId>org.broadinstitute</groupId>
+  <artifactId>variant</artifactId>
+  <name>variant</name>
+  <version>1.105.1642</version>
+</project>
diff --git a/settings/repository/com.google.code.caliper/caliper-1.0-SNAPSHOT.xml b/settings/repository/com.google.code.caliper/caliper-1.0-SNAPSHOT.xml
deleted file mode 100644
index 0e2b727e1..000000000
--- a/settings/repository/com.google.code.caliper/caliper-1.0-SNAPSHOT.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="com.google.code.caliper" module="caliper" revision="1.0-SNAPSHOT" status="integration" publication="20110609114800" />
-</ivy-module>
diff --git a/settings/repository/com.google.code.cofoja/cofoja-1.0-r139.xml b/settings/repository/com.google.code.cofoja/cofoja-1.0-r139.xml
deleted file mode 100644
index 202d3d0a3..000000000
--- a/settings/repository/com.google.code.cofoja/cofoja-1.0-r139.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="com.google.code.cofoja" module="cofoja" revision="1.0-r139" status="integration" publication="20110609114800" />
-</ivy-module>
diff --git a/settings/repository/edu.mit.broad/picard-private-parts-2872.jar b/settings/repository/edu.mit.broad/picard-private-parts-2872.jar
deleted file mode 100644
index b6e685684..000000000
Binary files a/settings/repository/edu.mit.broad/picard-private-parts-2872.jar and /dev/null differ
diff --git a/settings/repository/edu.mit.broad/picard-private-parts-2872.xml b/settings/repository/edu.mit.broad/picard-private-parts-2872.xml
deleted file mode 100644
index 677d27d80..000000000
--- a/settings/repository/edu.mit.broad/picard-private-parts-2872.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="edu.mit.broad" module="picard-private-parts" revision="2872" status="integration" publication="" />
-</ivy-module>
diff --git a/settings/repository/gov.nist/Jama-1.0.2.xml b/settings/repository/gov.nist/Jama-1.0.2.xml
deleted file mode 100644
index 57ea106ea..000000000
--- a/settings/repository/gov.nist/Jama-1.0.2.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="gov.nist" module="Jama" revision="1.0.2" status="release" />
-</ivy-module>
diff --git a/settings/repository/net.sf.gridscheduler/drmaa-6.2u5p2.xml b/settings/repository/net.sf.gridscheduler/drmaa-6.2u5p2.xml
deleted file mode 100644
index c6a8da052..000000000
--- a/settings/repository/net.sf.gridscheduler/drmaa-6.2u5p2.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf.gridscheduler" module="drmaa" revision="6.2u5p2" status="release" />
-</ivy-module>
diff --git a/settings/repository/net.sf.snpeff/snpeff-2.0.5.xml b/settings/repository/net.sf.snpeff/snpeff-2.0.5.xml
deleted file mode 100644
index 9a622abe5..000000000
--- a/settings/repository/net.sf.snpeff/snpeff-2.0.5.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf.snpeff" module="snpeff" revision="2.0.5" status="release" />
-</ivy-module>
diff --git a/settings/repository/net.sf/picard-1.104.1628.xml b/settings/repository/net.sf/picard-1.104.1628.xml
deleted file mode 100644
index bd0c9fbcd..000000000
--- a/settings/repository/net.sf/picard-1.104.1628.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf" module="picard" revision="1.104.1628" status="release" />
-</ivy-module>
diff --git a/settings/repository/net.sf/sam-1.104.1628.xml b/settings/repository/net.sf/sam-1.104.1628.xml
deleted file mode 100644
index 0b0cba93f..000000000
--- a/settings/repository/net.sf/sam-1.104.1628.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf" module="sam" revision="1.104.1628" status="release" />
-</ivy-module>
diff --git a/settings/repository/org.broad/tribble-1.104.1628.xml b/settings/repository/org.broad/tribble-1.104.1628.xml
deleted file mode 100644
index c2158e974..000000000
--- a/settings/repository/org.broad/tribble-1.104.1628.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="org.broad" module="tribble" revision="1.104.1628" status="integration" />
-</ivy-module>
diff --git a/settings/repository/org.broadinstitute/variant-1.105.1642.xml b/settings/repository/org.broadinstitute/variant-1.105.1642.xml
deleted file mode 100644
index d1846ce23..000000000
--- a/settings/repository/org.broadinstitute/variant-1.105.1642.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="org.broadinstitute" module="variant" revision="1.105.1642" status="integration" />
-</ivy-module>