diff --git a/tools/cooja/java/se/sics/cooja/util/ExecuteJAR.java b/tools/cooja/java/se/sics/cooja/util/ExecuteJAR.java
index d7f088717..53220d53e 100644
--- a/tools/cooja/java/se/sics/cooja/util/ExecuteJAR.java
+++ b/tools/cooja/java/se/sics/cooja/util/ExecuteJAR.java
@@ -24,26 +24,28 @@
  * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
  * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  *
- * $Id: ExecuteJAR.java,v 1.9 2010/03/19 12:34:37 fros4943 Exp $
+ * $Id: ExecuteJAR.java,v 1.10 2010/03/19 15:02:26 fros4943 Exp $
  */
 
 package se.sics.cooja.util;
 
 import java.io.File;
-import java.io.FileNotFoundException;
 import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.InputStream;
 import java.net.URISyntaxException;
 import java.security.AccessControlException;
 import java.util.Enumeration;
+import java.util.List;
 import java.util.Properties;
 
 import org.apache.log4j.BasicConfigurator;
 import org.apache.log4j.Logger;
 import org.apache.log4j.xml.DOMConfigurator;
+import org.jdom.Attribute;
 import org.jdom.Document;
 import org.jdom.Element;
+import org.jdom.input.SAXBuilder;
 import org.jdom.output.Format;
 import org.jdom.output.XMLOutputter;
 
@@ -63,7 +65,6 @@ public class ExecuteJAR {
   public final static String SIMCONFIG_FILENAME = "simulation.csc";
   public final static String EXTERNALTOOLS_FILENAME = "exttools.config";
   public final static String PROJECT_DEFAULT_CONFIG_FILENAME = "cooja_default.config";
-  public final static String FIRMWARE_SUFFIX = ".sky";
 
   public static void main(String[] args) {
     try {
@@ -113,7 +114,7 @@ public class ExecuteJAR {
     try {
       buildExecutableJAR(s.getGUI(), jar);
     } catch (RuntimeException e) {
-      logger.fatal(e.getMessage());
+      logger.fatal(e.getMessage(), e);
       System.exit(1);
     }
     System.exit(0);
@@ -176,33 +177,10 @@ public class ExecuteJAR {
       }
       GUI.externalToolsUserSettingsFile = diskFile;
 
-      int firmwareCounter = 0;
-      while (true) {
-        File firmwareFile = new File(firmwareCounter + FIRMWARE_SUFFIX);
-        diskFile = new File(executeDir, firmwareCounter + FIRMWARE_SUFFIX);
-        firmwareCounter++;
-        if (OVERWRITE || !diskFile.exists()) {
-          logger.info("Unpacking firmware file: " + firmwareFile.getName() + " -> " + diskFile.getName());
-          inputStream = GUI.class.getResourceAsStream("/" + firmwareFile.getName());
-          if (inputStream == null) {
-            /* Not available in simulation */
-            break;
-          }
-          byte[] fileData = ArrayUtils.readFromStream(inputStream);
-          if (fileData == null) {
-            logger.info("Failed extracting file (read fail)");
-            System.exit(1);
-          }
-          boolean ok = ArrayUtils.writeToFile(diskFile, fileData);
-          if (!ok) {
-            logger.info("Failed extracting file (write fail)");
-            System.exit(1);
-          }
-        } else {
-          logger.info("Skip: firmware files already exist: " + diskFile);
-          break;
-        }
-      }
+      /* Unpack files from JAR (with attribute EXPORT=copy) */
+      SAXBuilder builder = new SAXBuilder();
+      Document doc = builder.build(new File(executeDir, SIMCONFIG_FILENAME));
+      handleExportAttributesFromJAR(doc.getRootElement(), new File(executeDir, SIMCONFIG_FILENAME), new File(executeDir));
     } catch (Exception e) {
       logger.fatal("Error when unpacking executable JAR: " + e.getMessage());
       return;
@@ -334,49 +312,7 @@ public class ExecuteJAR {
     /* Prepare simulation config */
     Element rootElement = gui.extractSimulationConfig();
     logger.info("Extracting simulation configuration");
-    logger.info("Simconfig: Stripping project references");
-    rootElement.removeChildren("project"); /* Remove project references */
-    for (Object simElement : rootElement.getChildren()) {
-      if (((Element) simElement).getName().equals("simulation")) {
-        int firmwareCounter = 0;
-        for (Object moteTypeElement : ((Element)simElement).getChildren()) {
-          if (((Element) moteTypeElement).getName().equals("motetype")) {
-            logger.info("Simconfig: Stripping source references");
-            logger.info("Simconfig: Stripping build commands");
-            ((Element)moteTypeElement).removeChildren("source"); /* Remove source references */
-            ((Element)moteTypeElement).removeChildren("commands"); /* Remove build commands */
-            for (Object pathElement : ((Element)moteTypeElement).getChildren()) {
-              if (((Element) pathElement).getName().equals("firmware")) {
-                String newName = (firmwareCounter++) + FIRMWARE_SUFFIX;
-                /* Copy firmwares, and update firmware references */
-                String firmwarePath = ((Element)pathElement).getText();
-                File firmwareFile = gui.restorePortablePath(new File(firmwarePath));
-                if (!firmwareFile.exists()) {
-                  throw new RuntimeException(
-                      "Firmware file does not exist: " + firmwareFile
-                  );
-                }     
-                logger.info("Simconfig: Copying firmware file: " + firmwareFile.getAbsolutePath());
-                byte[] data = ArrayUtils.readFromFile(firmwareFile);
-                if (data == null) {
-                  throw new RuntimeException(
-                      "Error when reading firmware file: " + firmwareFile
-                  );
-                }
-                boolean ok = ArrayUtils.writeToFile(new File(workingDir, newName), data);
-                if (!ok) {
-                  throw new RuntimeException(
-                      "Error when writing firmware file: " + firmwareFile
-                  );
-                }
-                logger.info("Simconfig: Update firmware path reference: " + firmwareFile.getAbsolutePath() + " -> " + ("[CONFIG_DIR]/" + newName));
-                ((Element)pathElement).setText("[CONFIG_DIR]/" + newName);
-              }
-            }
-          }
-        }
-      }
-    }
+    handleExportAttributesToJAR(rootElement, gui, workingDir);
 
     /* Save simulation config */
     File configFile = new File(workingDir, SIMCONFIG_FILENAME);
@@ -506,7 +442,79 @@ public class ExecuteJAR {
     logger.info("Done! To run simulation: > java -jar " + outputFile.getName());
     return true;
   }
+
+  private static void handleExportAttributesToJAR(Element e, GUI gui, File toDir) {
+    /* Checks configuration for EXPORT attributes:
+     * copy: file copy file to exported JAR, update file path.
+     * discard: remove config element */
+    
+    for (Element c : ((List<Element>) e.getChildren()).toArray(new Element[0])) {
+      Attribute a = c.getAttribute("EXPORT");
+      if (a != null && a.getValue().equals("copy")) {
+        /* Copy file to JAR */
+        File file = gui.restorePortablePath(new File(c.getText()));
+        if (!file.exists()) {
+          throw new RuntimeException("File not found: " + file);
+        }     
+        byte[] data = ArrayUtils.readFromFile(file);
+        if (data == null) {
+          throw new RuntimeException("Could not copy file: " + file);
+        }
+
+        String newFilename = file.getName();
+        while (new File(toDir, newFilename).exists()) {
+          newFilename += "-1";
+        }
+        boolean ok = ArrayUtils.writeToFile(new File(toDir, newFilename), data);
+        if (!ok) {
+          throw new RuntimeException("Error when copying file: " + file);
+        }
+        logger.info("Simconfig: Copied file: " + file.getAbsolutePath() + " -> " + ("[CONFIG_DIR]/" + newFilename));
+        ((Element)c).setText("[CONFIG_DIR]/" + newFilename);
+      } else if (a != null && a.getValue().equals("discard")) {
+        /* Remove config element */
+        e.removeChild(c.getName());
+        logger.info("Simconfig: Discarded element '" + c.getName() + "': " + c.getText());
+        continue;
+      } else if (a != null) {
+        throw new RuntimeException("Unknown EXPORT attribute value: " + a.getValue());
+      }
+      
+      /* Recursive search */
+      handleExportAttributesToJAR(c, gui, toDir);
+    }
+  }
   
+  private static void handleExportAttributesFromJAR(Element e, File config, File toDir) {
+    for (Element c : ((List<Element>) e.getChildren()).toArray(new Element[0])) {
+      Attribute a = c.getAttribute("EXPORT");
+      if (a != null && a.getValue().equals("copy")) {
+        /* Copy file from JAR */
+        File file = GUI.restoreConfigRelativePath(config, new File(c.getText()));
+        InputStream inputStream = GUI.class.getResourceAsStream("/" + file.getName());
+        if (inputStream == null) {
+          throw new RuntimeException("Could not unpack file: " + file);
+        }
+        byte[] fileData = ArrayUtils.readFromStream(inputStream);
+        if (fileData == null) {
+          logger.info("Failed unpacking file");
+          throw new RuntimeException("Could not unpack file: " + file);
+        }
+        if (OVERWRITE || !file.exists()) {
+          boolean ok = ArrayUtils.writeToFile(file, fileData);
+          if (!ok) {
+            throw new RuntimeException("Failed unpacking file: " + file);
+          }
+          logger.info("Unpacked file from JAR: " + file.getName());
+        } else if (OVERWRITE) {
+          logger.info("Skip: unpack file from JAR: " + file.getName());
+        }
+      }
+      
+      /* Recursive search */
+      handleExportAttributesFromJAR(c, config, toDir);
+    }
+  }
   private static boolean deleteDirectory(File path) {
     if(path.exists()) {
       File[] files = path.listFiles();