Index: unix_installer/upgrader-package/ant-scripts/update-deploy-tools.xml
===================================================================
diff -u -rb813ae3d1466f6848b2a2ea6bf8551f8494cc4dd -r80349002d46efb898c06fc8835c074d6418be97e
--- unix_installer/upgrader-package/ant-scripts/update-deploy-tools.xml	(.../update-deploy-tools.xml)	(revision b813ae3d1466f6848b2a2ea6bf8551f8494cc4dd)
+++ unix_installer/upgrader-package/ant-scripts/update-deploy-tools.xml	(.../update-deploy-tools.xml)	(revision 80349002d46efb898c06fc8835c074d6418be97e)
@@ -70,20 +70,42 @@
 		
 	</target>
 	
+	<target name="update-custom-tool-contexts" description="Updates the web.xmls for the non-custom tools">
+        <echo>Updating web.xml and MANIFEST.MF for lams-central.war, lams-monitor.war and lams-learning.war. using for custom tools</echo>
+        <path id="deploy.lib.classpath">
+            <fileset dir="${deploy.tool.dir}">
+                <include name="lib/*.jar"/>
+            </fileset>
+        </path> 
+        
+        <java classname="org.lamsfoundation.lams.tool.deploy.AddCustomWebXmlContexts" classpathref="deploy.lib.classpath" fork="true">
+            <arg value="${jboss.deploy}" />
+            <arg value="${db.username}" />
+            <arg value="${db.password}" />
+            <arg value="${SQL_URL}" />
+        </java> 
+    </target>
 	
-	
-	<target name="update-application-xml" description="Removes unneccessary modules from application.xml">
+	<target name="update-application-xml" description="Adds/Removes java modules to application.xml">
 		<path id="deploy.lib.classpath">
 			<fileset dir="${deploy.tool.dir}">
 				<include name="lib/*.jar"/>
 			</fileset>
 		</path>
 		
-		<echo>Updating application.xml</echo>
+		<!-- 2.1 SPECIFIC UPDATE!!!!!!!!!!!! -->
+		<echo>BEGIN Updating application.xml</echo>
+		<java classname="org.lamsfoundation.lams.tool.deploy.AddModuleToApplicationXmlTask" classpathref="deploy.lib.classpath" fork="true">
+			<arg value="${jboss.deploy}" />
+			<arg value="commons-io-1.4.jar" />
+		</java>
+		<!-- END 2.1 SPECIFIC UPDATE!!!!!!!!!!!! -->
 		
+		<!-- 2.0.4 SPECIFIC UPDATE!!!!!!!!!!!! 
 		<java classname="org.lamsfoundation.lams.tool.deploy.RemoveModuleFromApplicationXmlTask" classpathref="deploy.lib.classpath" fork="true">
 			<arg value="${jboss.deploy}" />
 		</java>
+		END 2.0.4 SPECIFIC UPDATE!!!!!!!!!!!! -->
 		
 	</target>
 	
@@ -115,6 +137,7 @@
 			<fileset dir="${jboss.deploy}/lams-monitoring.war.tmp">
 				<include name="*"/>
 				<include name="css/*"/>
+				<include name="branching/*"/>
 				<include name="gate/*"/>
 				<include name="grouping/*"/>
 				<include name="images/*"/>
@@ -138,6 +161,7 @@
 			<fileset dir="${jboss.deploy}/lams-learning.war.tmp">
 				<include name="*"/>
 				<include name="css/*"/>
+				<include name="branching/*"/>
 				<include name="exportPortfolio/*"/>
 				<include name="notebook/*"/>
 				<include name="gate/*"/>
@@ -148,8 +172,10 @@
 			</fileset>
 		</war>
 		
+		
 		<delete dir="${jboss.deploy}/lams-learning.war.tmp" failonerror="false" />
 		<delete dir="${jboss.deploy}/lams-monitoring.war.tmp" failonerror="false" />
+		
 	</target>
 			
 	<target name="deploy-tool" description="runs the tool deployer for a given tool">