Index: unix_installer/upgrader-package/java/backup.java
===================================================================
diff -u -rdfde3b7525955235b664ca801fdece4fb418b532 -r93b5a921b65de778d5151605132f85683deb0741
--- unix_installer/upgrader-package/java/backup.java	(.../backup.java)	(revision dfde3b7525955235b664ca801fdece4fb418b532)
+++ unix_installer/upgrader-package/java/backup.java	(.../backup.java)	(revision 93b5a921b65de778d5151605132f85683deb0741)
@@ -7,7 +7,7 @@
 	
 	private BufferedReader in;
 	
-	private String backupdir, jbossdir;
+	private String backupdir, jbossdir, repositoryDir, etcdir;
 
 	public String mysqldir, dbuser, dbname, dbpass, dburl;
 
@@ -30,6 +30,8 @@
 		{
 			System.out.println("Copying files from " + jbossdir + "/ to " + backupdir + "/jboss-4.0.2/ ...");
 			copyFiles(jbossdir + "/", backupdir+"/jboss-4.0.2/");
+			copyFiles(etcdir + "/", backupdir+"/ectlams2/");
+			copyFiles(repositoryDir + "/", backupdir+"/repository/");
 			System.out.println("Done.\n");
 		}
 		catch (IOException e)
@@ -52,6 +54,8 @@
 			Properties lamsProperties = new Properties();
 			lamsProperties.load(new FileInputStream("lams.properties"));		
 			jbossdir = lamsProperties.getProperty("JBOSS_DIR");
+			repositoryDir = lamsProperties.getProperty("LAMS_DIR") + "/repository";
+			etcdir = "/etc/lams2";
 			mysqldir = lamsProperties.getProperty("SQL_DIR");
 			dbname = lamsProperties.getProperty("DB_NAME");
 			dbuser = lamsProperties.getProperty("DB_USER");
@@ -154,30 +158,29 @@
 	// The method copyFiles being defined
 	public void copyFiles(String strPath, String dstPath) throws IOException
 	{
-		
-  
 		File src = new File(strPath);
 		File dest = new File(dstPath);
 	
-		if (src.isDirectory())
+		if (src.exists())
 		{
-			System.out.println("Copying: " + src.getAbsolutePath());
-			dest.mkdirs();
-			String list[] = src.list();
-		
-		
-		
-			for (int i = 0; i < list.length; i++)
+			if (src.isDirectory())
 			{
-				String dest1 = dest.getAbsolutePath() + "/" + list[i];
-				String src1 = src.getAbsolutePath() + "/" + list[i];
-				copyFiles(src1 , dest1);
+				System.out.println("Copying: " + src.getAbsolutePath());
+				dest.mkdirs();
+				String list[] = src.list();
+			
+				for (int i = 0; i < list.length; i++)
+				{
+					String dest1 = dest.getAbsolutePath() + "/" + list[i];
+					String src1 = src.getAbsolutePath() + "/" + list[i];
+					copyFiles(src1 , dest1);
+				}
 			}
+			else
+			{
+	 			copy(src, dest);
+			}
 		}
-		else
-		{
- 			copy(src, dest);
-		}
 	}
 
 	public void copy(File source, File target) throws IOException
Index: unix_installer/upgrader-package/update-lams.sh
===================================================================
diff -u -rd3e1423ab32ceafba2ea46b790b7206c6e8dbfad -r93b5a921b65de778d5151605132f85683deb0741
--- unix_installer/upgrader-package/update-lams.sh	(.../update-lams.sh)	(revision d3e1423ab32ceafba2ea46b790b7206c6e8dbfad)
+++ unix_installer/upgrader-package/update-lams.sh	(.../update-lams.sh)	(revision 93b5a921b65de778d5151605132f85683deb0741)
@@ -285,7 +285,8 @@
 backup()
 {
     printf "\nDo you wish to automatically backup lams before updating? (Recommended. NOTE: Requires MySql to be installed at localhost)\n"
-    printf "The space required to backup your LAMS installation: \n"
+    printf "Please check the below directories are correct before running this backup. If they are not, quit the installer and backup LAMS manually.\n"
+    printf "The space required to backup your LAMS installation:\n"
     du -chs $LAMS_DIR $JBOSS_DIR
     printf "(y)es I wish to backup LAMS.\n"
     printf "(n)o I have already backed up LAMS, I am ready to update.\n"
@@ -309,18 +310,18 @@
         
         $JDK_DIR/bin/java -cp bin backup
         if [  "$?" -ne  "0" ]
-                then
-                        echo "Update failed, please check that LAMS $REQ_LAMS_VERSION is installed and your lams.properties file is correct."
-                        installfailed
-                fi
+        then
+                echo "Update failed, Failed to backup LAMS."
+                installfailed
+        fi
 
         chmod 755 bin/lamsdump.sql
         bin/lamsdump.sql
         if [  "$?" -ne  "0" ]
-                then
-                        echo "Update failed, please check that LAMS $REQ_LAMS_VERSION is installed and your lams.properties file is correct."
-                        installfailed
-                fi
+        then
+                echo "Update failed, problem dumping database for backup."
+                installfailed
+        fi
 
         ;;
     n)