diff --git a/.idea/.name b/.idea/.name
deleted file mode 100644
index 7014f65a5..000000000
--- a/.idea/.name
+++ /dev/null
@@ -1 +0,0 @@
-cmi-gatk
\ No newline at end of file
diff --git a/.idea/ant.xml b/.idea/ant.xml
deleted file mode 100644
index 4674eeac9..000000000
--- a/.idea/ant.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="AntConfiguration">
-    <defaultAnt bundledAnt="true" />
-    <buildFile url="file://$PROJECT_DIR$/build.xml">
-      <additionalClassPath />
-      <antReference projectDefault="true" />
-      <customJdkName value="" />
-      <maximumHeapSize value="128" />
-      <maximumStackSize value="2" />
-      <properties />
-    </buildFile>
-  </component>
-</project>
-
diff --git a/.idea/codeStyleSettings.xml b/.idea/codeStyleSettings.xml
deleted file mode 100644
index 9178b389f..000000000
--- a/.idea/codeStyleSettings.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="ProjectCodeStyleSettingsManager">
-    <option name="PER_PROJECT_SETTINGS">
-      <value>
-        <XML>
-          <option name="XML_LEGACY_SETTINGS_IMPORTED" value="true" />
-        </XML>
-      </value>
-    </option>
-  </component>
-</project>
-
diff --git a/.idea/compiler.xml b/.idea/compiler.xml
deleted file mode 100644
index ded2e9a1d..000000000
--- a/.idea/compiler.xml
+++ /dev/null
@@ -1,21 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="CompilerConfiguration">
-    <option name="DEFAULT_COMPILER" value="Javac" />
-    <resourceExtensions />
-    <wildcardResourcePatterns>
-      <entry name="?*.properties" />
-      <entry name="?*.xml" />
-      <entry name="?*.gif" />
-      <entry name="?*.png" />
-      <entry name="?*.jpeg" />
-      <entry name="?*.jpg" />
-      <entry name="?*.html" />
-      <entry name="?*.dtd" />
-      <entry name="?*.tld" />
-      <entry name="?*.ftl" />
-    </wildcardResourcePatterns>
-    <annotationProcessing enabled="true" useClasspath="true" />
-  </component>
-</project>
-
diff --git a/.idea/copyright/profiles_settings.xml b/.idea/copyright/profiles_settings.xml
deleted file mode 100644
index 3572571ad..000000000
--- a/.idea/copyright/profiles_settings.xml
+++ /dev/null
@@ -1,5 +0,0 @@
-<component name="CopyrightManager">
-  <settings default="">
-    <module2copyright />
-  </settings>
-</component>
\ No newline at end of file
diff --git a/.idea/encodings.xml b/.idea/encodings.xml
deleted file mode 100644
index e206d70d8..000000000
--- a/.idea/encodings.xml
+++ /dev/null
@@ -1,5 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="Encoding" useUTFGuessing="true" native2AsciiForPropertiesFiles="false" />
-</project>
-
diff --git a/.idea/highlighting.xml b/.idea/highlighting.xml
deleted file mode 100644
index f33b64d94..000000000
--- a/.idea/highlighting.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="HighlightingAdvisor">
-    <option name="SUGGEST_TYPE_AWARE_HIGHLIGHTING" value="false" />
-    <option name="TYPE_AWARE_HIGHLIGHTING_ENABLED" value="true" />
-  </component>
-</project>
-
diff --git a/.idea/inspectionProfiles/Project_Default.xml b/.idea/inspectionProfiles/Project_Default.xml
deleted file mode 100644
index b8c243dbe..000000000
--- a/.idea/inspectionProfiles/Project_Default.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<component name="InspectionProjectProfileManager">
-  <profile version="1.0" is_locked="false">
-    <option name="myName" value="Project Default" />
-    <option name="myLocal" value="false" />
-    <inspection_tool class="SpellCheckingInspection" enabled="false" level="TYPO" enabled_by_default="false">
-      <option name="processCode" value="true" />
-      <option name="processLiterals" value="false" />
-      <option name="processComments" value="true" />
-    </inspection_tool>
-  </profile>
-</component>
\ No newline at end of file
diff --git a/.idea/inspectionProfiles/profiles_settings.xml b/.idea/inspectionProfiles/profiles_settings.xml
deleted file mode 100644
index 3b312839b..000000000
--- a/.idea/inspectionProfiles/profiles_settings.xml
+++ /dev/null
@@ -1,7 +0,0 @@
-<component name="InspectionProjectProfileManager">
-  <settings>
-    <option name="PROJECT_PROFILE" value="Project Default" />
-    <option name="USE_PROJECT_PROFILE" value="true" />
-    <version value="1.0" />
-  </settings>
-</component>
\ No newline at end of file
diff --git a/.idea/libraries/GATK_libraries.xml b/.idea/libraries/GATK_libraries.xml
deleted file mode 100644
index b363bbe6c..000000000
--- a/.idea/libraries/GATK_libraries.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<component name="libraryTable">
-  <library name="GATK libraries">
-    <CLASSES>
-      <root url="file://$PROJECT_DIR$/lib" />
-    </CLASSES>
-    <JAVADOC />
-    <SOURCES>
-      <root url="file://$PROJECT_DIR$/../../picard/src/java" />
-    </SOURCES>
-    <jarDirectory url="file://$PROJECT_DIR$/lib" recursive="false" />
-  </library>
-</component>
\ No newline at end of file
diff --git a/.idea/misc.xml b/.idea/misc.xml
deleted file mode 100644
index a79280c52..000000000
--- a/.idea/misc.xml
+++ /dev/null
@@ -1,32 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="EntryPointsManager">
-    <entry_points version="2.0" />
-  </component>
-  <component name="IdProvider" IDEtalkID="1AD151C138300C50536BAE046D66308C" />
-  <component name="JavadocGenerationManager">
-    <option name="OUTPUT_DIRECTORY" />
-    <option name="OPTION_SCOPE" value="protected" />
-    <option name="OPTION_HIERARCHY" value="true" />
-    <option name="OPTION_NAVIGATOR" value="true" />
-    <option name="OPTION_INDEX" value="true" />
-    <option name="OPTION_SEPARATE_INDEX" value="true" />
-    <option name="OPTION_DOCUMENT_TAG_USE" value="false" />
-    <option name="OPTION_DOCUMENT_TAG_AUTHOR" value="false" />
-    <option name="OPTION_DOCUMENT_TAG_VERSION" value="false" />
-    <option name="OPTION_DOCUMENT_TAG_DEPRECATED" value="true" />
-    <option name="OPTION_DEPRECATED_LIST" value="true" />
-    <option name="OTHER_OPTIONS" value="" />
-    <option name="HEAP_SIZE" />
-    <option name="LOCALE" />
-    <option name="OPEN_IN_BROWSER" value="true" />
-  </component>
-  <component name="ProjectResources">
-    <default-html-doctype>http://www.w3.org/1999/xhtml</default-html-doctype>
-  </component>
-  <component name="ProjectRootManager" version="2" languageLevel="JDK_1_6" assert-keyword="true" jdk-15="true" project-jdk-name="1.6" project-jdk-type="JavaSDK">
-    <output url="file://$PROJECT_DIR$/out" />
-  </component>
-  <component name="WebServicesPlugin" addRequiredLibraries="true" />
-</project>
-
diff --git a/.idea/modules.xml b/.idea/modules.xml
deleted file mode 100644
index 09caa2933..000000000
--- a/.idea/modules.xml
+++ /dev/null
@@ -1,9 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="ProjectModuleManager">
-    <modules>
-      <module fileurl="file://$PROJECT_DIR$/cmi-gatk.iml" filepath="$PROJECT_DIR$/cmi-gatk.iml" />
-    </modules>
-  </component>
-</project>
-
diff --git a/.idea/scopes/scope_settings.xml b/.idea/scopes/scope_settings.xml
deleted file mode 100644
index 922003b84..000000000
--- a/.idea/scopes/scope_settings.xml
+++ /dev/null
@@ -1,5 +0,0 @@
-<component name="DependencyValidationManager">
-  <state>
-    <option name="SKIP_IMPORT_STATEMENTS" value="false" />
-  </state>
-</component>
\ No newline at end of file
diff --git a/.idea/uiDesigner.xml b/.idea/uiDesigner.xml
deleted file mode 100644
index 3b0002030..000000000
--- a/.idea/uiDesigner.xml
+++ /dev/null
@@ -1,125 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="Palette2">
-    <group name="Swing">
-      <item class="com.intellij.uiDesigner.HSpacer" tooltip-text="Horizontal Spacer" icon="/com/intellij/uiDesigner/icons/hspacer.png" removable="false" auto-create-binding="false" can-attach-label="false">
-        <default-constraints vsize-policy="1" hsize-policy="6" anchor="0" fill="1" />
-      </item>
-      <item class="com.intellij.uiDesigner.VSpacer" tooltip-text="Vertical Spacer" icon="/com/intellij/uiDesigner/icons/vspacer.png" removable="false" auto-create-binding="false" can-attach-label="false">
-        <default-constraints vsize-policy="6" hsize-policy="1" anchor="0" fill="2" />
-      </item>
-      <item class="javax.swing.JPanel" icon="/com/intellij/uiDesigner/icons/panel.png" removable="false" auto-create-binding="false" can-attach-label="false">
-        <default-constraints vsize-policy="3" hsize-policy="3" anchor="0" fill="3" />
-      </item>
-      <item class="javax.swing.JScrollPane" icon="/com/intellij/uiDesigner/icons/scrollPane.png" removable="false" auto-create-binding="false" can-attach-label="true">
-        <default-constraints vsize-policy="7" hsize-policy="7" anchor="0" fill="3" />
-      </item>
-      <item class="javax.swing.JButton" icon="/com/intellij/uiDesigner/icons/button.png" removable="false" auto-create-binding="true" can-attach-label="false">
-        <default-constraints vsize-policy="0" hsize-policy="3" anchor="0" fill="1" />
-        <initial-values>
-          <property name="text" value="Button" />
-        </initial-values>
-      </item>
-      <item class="javax.swing.JRadioButton" icon="/com/intellij/uiDesigner/icons/radioButton.png" removable="false" auto-create-binding="true" can-attach-label="false">
-        <default-constraints vsize-policy="0" hsize-policy="3" anchor="8" fill="0" />
-        <initial-values>
-          <property name="text" value="RadioButton" />
-        </initial-values>
-      </item>
-      <item class="javax.swing.JCheckBox" icon="/com/intellij/uiDesigner/icons/checkBox.png" removable="false" auto-create-binding="true" can-attach-label="false">
-        <default-constraints vsize-policy="0" hsize-policy="3" anchor="8" fill="0" />
-        <initial-values>
-          <property name="text" value="CheckBox" />
-        </initial-values>
-      </item>
-      <item class="javax.swing.JLabel" icon="/com/intellij/uiDesigner/icons/label.png" removable="false" auto-create-binding="false" can-attach-label="false">
-        <default-constraints vsize-policy="0" hsize-policy="0" anchor="8" fill="0" />
-        <initial-values>
-          <property name="text" value="Label" />
-        </initial-values>
-      </item>
-      <item class="javax.swing.JTextField" icon="/com/intellij/uiDesigner/icons/textField.png" removable="false" auto-create-binding="true" can-attach-label="true">
-        <default-constraints vsize-policy="0" hsize-policy="6" anchor="8" fill="1">
-          <preferred-size width="150" height="-1" />
-        </default-constraints>
-      </item>
-      <item class="javax.swing.JPasswordField" icon="/com/intellij/uiDesigner/icons/passwordField.png" removable="false" auto-create-binding="true" can-attach-label="true">
-        <default-constraints vsize-policy="0" hsize-policy="6" anchor="8" fill="1">
-          <preferred-size width="150" height="-1" />
-        </default-constraints>
-      </item>
-      <item class="javax.swing.JFormattedTextField" icon="/com/intellij/uiDesigner/icons/formattedTextField.png" removable="false" auto-create-binding="true" can-attach-label="true">
-        <default-constraints vsize-policy="0" hsize-policy="6" anchor="8" fill="1">
-          <preferred-size width="150" height="-1" />
-        </default-constraints>
-      </item>
-      <item class="javax.swing.JTextArea" icon="/com/intellij/uiDesigner/icons/textArea.png" removable="false" auto-create-binding="true" can-attach-label="true">
-        <default-constraints vsize-policy="6" hsize-policy="6" anchor="0" fill="3">
-          <preferred-size width="150" height="50" />
-        </default-constraints>
-      </item>
-      <item class="javax.swing.JTextPane" icon="/com/intellij/uiDesigner/icons/textPane.png" removable="false" auto-create-binding="true" can-attach-label="true">
-        <default-constraints vsize-policy="6" hsize-policy="6" anchor="0" fill="3">
-          <preferred-size width="150" height="50" />
-        </default-constraints>
-      </item>
-      <item class="javax.swing.JEditorPane" icon="/com/intellij/uiDesigner/icons/editorPane.png" removable="false" auto-create-binding="true" can-attach-label="true">
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-          <preferred-size width="150" height="50" />
-        </default-constraints>
-      </item>
-      <item class="javax.swing.JComboBox" icon="/com/intellij/uiDesigner/icons/comboBox.png" removable="false" auto-create-binding="true" can-attach-label="true">
-        <default-constraints vsize-policy="0" hsize-policy="2" anchor="8" fill="1" />
-      </item>
-      <item class="javax.swing.JTable" icon="/com/intellij/uiDesigner/icons/table.png" removable="false" auto-create-binding="true" can-attach-label="false">
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-          <preferred-size width="150" height="50" />
-        </default-constraints>
-      </item>
-      <item class="javax.swing.JList" icon="/com/intellij/uiDesigner/icons/list.png" removable="false" auto-create-binding="true" can-attach-label="false">
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-          <preferred-size width="150" height="50" />
-        </default-constraints>
-      </item>
-      <item class="javax.swing.JTree" icon="/com/intellij/uiDesigner/icons/tree.png" removable="false" auto-create-binding="true" can-attach-label="false">
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-      </item>
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-          <preferred-size width="200" height="200" />
-        </default-constraints>
-      </item>
-      <item class="javax.swing.JSpinner" icon="/com/intellij/uiDesigner/icons/spinner.png" removable="false" auto-create-binding="true" can-attach-label="true">
-        <default-constraints vsize-policy="0" hsize-policy="6" anchor="8" fill="1" />
-      </item>
-      <item class="javax.swing.JSlider" icon="/com/intellij/uiDesigner/icons/slider.png" removable="false" auto-create-binding="true" can-attach-label="false">
-        <default-constraints vsize-policy="0" hsize-policy="6" anchor="8" fill="1" />
-      </item>
-      <item class="javax.swing.JSeparator" icon="/com/intellij/uiDesigner/icons/separator.png" removable="false" auto-create-binding="false" can-attach-label="false">
-        <default-constraints vsize-policy="6" hsize-policy="6" anchor="0" fill="3" />
-      </item>
-      <item class="javax.swing.JProgressBar" icon="/com/intellij/uiDesigner/icons/progressbar.png" removable="false" auto-create-binding="true" can-attach-label="false">
-        <default-constraints vsize-policy="0" hsize-policy="6" anchor="0" fill="1" />
-      </item>
-      <item class="javax.swing.JToolBar" icon="/com/intellij/uiDesigner/icons/toolbar.png" removable="false" auto-create-binding="false" can-attach-label="false">
-        <default-constraints vsize-policy="0" hsize-policy="6" anchor="0" fill="1">
-          <preferred-size width="-1" height="20" />
-        </default-constraints>
-      </item>
-      <item class="javax.swing.JToolBar$Separator" icon="/com/intellij/uiDesigner/icons/toolbarSeparator.png" removable="false" auto-create-binding="false" can-attach-label="false">
-        <default-constraints vsize-policy="0" hsize-policy="0" anchor="0" fill="1" />
-      </item>
-      <item class="javax.swing.JScrollBar" icon="/com/intellij/uiDesigner/icons/scrollbar.png" removable="false" auto-create-binding="true" can-attach-label="false">
-        <default-constraints vsize-policy="6" hsize-policy="0" anchor="0" fill="2" />
-      </item>
-    </group>
-  </component>
-</project>
-
diff --git a/.idea/vcs.xml b/.idea/vcs.xml
deleted file mode 100644
index cbc984988..000000000
--- a/.idea/vcs.xml
+++ /dev/null
@@ -1,10 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="ClearCaseSharedConfig">
-    <option name="myUseUcmModel" value="true" />
-  </component>
-  <component name="VcsDirectoryMappings">
-    <mapping directory="" vcs="Git" />
-  </component>
-</project>
-
diff --git a/cmi-gatk.iml b/cmi-gatk.iml
deleted file mode 100644
index 4dbee1336..000000000
--- a/cmi-gatk.iml
+++ /dev/null
@@ -1,31 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<module type="JAVA_MODULE" version="4">
-  <component name="FacetManager">
-    <facet type="scala" name="Scala">
-      <configuration>
-        <option name="compilerLibraryLevel" value="Project" />
-        <option name="compilerLibraryName" value="GATK libraries" />
-      </configuration>
-    </facet>
-  </component>
-  <component name="NewModuleRootManager" inherit-compiler-output="true">
-    <exclude-output />
-    <content url="file://$MODULE_DIR$">
-      <sourceFolder url="file://$MODULE_DIR$/public/java/src" isTestSource="false" />
-      <sourceFolder url="file://$MODULE_DIR$/private/java/src" isTestSource="false" />
-      <sourceFolder url="file://$MODULE_DIR$/private/java/test" isTestSource="true" />
-      <sourceFolder url="file://$MODULE_DIR$/public/java/test" isTestSource="true" />
-      <sourceFolder url="file://$MODULE_DIR$/private/scala/src" isTestSource="false" />
-      <sourceFolder url="file://$MODULE_DIR$/public/scala/src" isTestSource="false" />
-      <sourceFolder url="file://$MODULE_DIR$/private/scala/test" isTestSource="true" />
-      <sourceFolder url="file://$MODULE_DIR$/public/scala/test" isTestSource="true" />
-      <sourceFolder url="file://$MODULE_DIR$/build/queue-extensions/src" isTestSource="false" />
-      <sourceFolder url="file://$MODULE_DIR$/protected/java/src" isTestSource="false" />
-      <sourceFolder url="file://$MODULE_DIR$/protected/java/test" isTestSource="true" />
-    </content>
-    <orderEntry type="inheritedJdk" />
-    <orderEntry type="sourceFolder" forTests="false" />
-    <orderEntry type="library" name="GATK libraries" level="project" />
-  </component>
-</module>
-
diff --git a/intellij_example.tar.bz2 b/intellij_example.tar.bz2
new file mode 100644
index 000000000..bce16045c
Binary files /dev/null and b/intellij_example.tar.bz2 differ