diff -r c07047c47ce9 autoupdate.services/libsrc/org/netbeans/updater/ModuleUpdater.java
--- a/autoupdate.services/libsrc/org/netbeans/updater/ModuleUpdater.java	Tue Mar 10 18:21:48 2009 +0300
+++ b/autoupdate.services/libsrc/org/netbeans/updater/ModuleUpdater.java	Wed Mar 11 13:26:40 2009 +0300
@@ -42,6 +42,7 @@
 package org.netbeans.updater;
 
 import java.io.*;
+import java.lang.reflect.Method;
 import java.util.*;
 import java.util.jar.*;
 
@@ -354,6 +355,8 @@
                 try {
                     jarFile = new JarFile (nbm);
                     Enumeration entries = jarFile.entries();
+                    List <String> list = new ArrayList <String> (jarFile.size());
+                    List <String> executableList = new ArrayList <String> ();
                     while( entries.hasMoreElements() ) {
                         JarEntry entry = (JarEntry) entries.nextElement();
                         checkStop();
@@ -375,14 +378,14 @@
                                     File bckFile = new File( getBackupDirectory (cluster), entry.getName() );
                                     bckFile.getParentFile ().mkdirs ();
                                     // System.out.println("Backing up" ); // NOI18N
-                                    copyStreams( new FileInputStream( destFile ), new FileOutputStream( bckFile ), -1 );
+                                    copyStreams( new FileInputStream( destFile ), bckFile, -1, list, executableList );
                                     if (!destFile.delete() && isWindows()) {
                                         trickyDeleteOnWindows(destFile);
                                     }
                                 } else {
                                     destFile.getParentFile ().mkdirs ();
                                 }
-                                bytesRead = copyStreams( jarFile.getInputStream( entry ), new FileOutputStream( destFile ), bytesRead );
+                                bytesRead = copyStreams( jarFile.getInputStream( entry ), destFile, bytesRead, list, executableList );
                                 UpdaterFrame.setProgressValue( bytesRead );
                             }
                         } else if ( entry.getName().startsWith( UPDATE_MAIN_DIR )&&
@@ -392,10 +395,11 @@
                                 entry.getName().substring(UPDATE_MAIN_DIR.length() + 1) );
                             destFile.getParentFile ().mkdirs ();
                             hasMainClass = true;
-                            bytesRead = copyStreams( jarFile.getInputStream( entry ), new FileOutputStream( destFile ), bytesRead );
+                            bytesRead = copyStreams( jarFile.getInputStream( entry ), destFile, bytesRead, list, executableList );
                             UpdaterFrame.setProgressValue( bytesRead );
                         }
                     }
+                    fixPermissions(list,executableList);
                     if ( hasMainClass ) {                    
                         MainConfig mconfig = new MainConfig (getMainDirString (cluster) + UpdateTracking.FILE_SEPARATOR + JVM_PARAMS_FILE, cluster);
                         if (mconfig.isValid()) {
@@ -532,6 +536,108 @@
     private String getMainDirString (File activeCluster) {
         return getMainDirectory (activeCluster).getPath ();
     }
+
+
+    private void fixPermissions(List<String> list, List <String> executableList) {
+        if (!isWindows() && !list.isEmpty()) {
+            List<String> commands = new ArrayList<String>();
+            commands.add("/usr/bin/file");
+            commands.addAll(list);
+
+            String filesInfo = readCommandOutput(commands);
+            List<String> fileExecutables = new ArrayList<String>();
+            for (String s : filesInfo.split("(?:\r\n|\n|\r)")) {//split by lines
+                int colonIndex = s.indexOf(":");
+                if (colonIndex != -1) {
+                    String filePath = s.substring(0, colonIndex).trim();
+                    String fileType = s.substring(colonIndex + 1);
+                    if (fileType.contains("executable") ||
+                            fileType.contains("dynamic lib") ||
+                            fileType.contains("shared object") ||
+                            fileType.contains("shared library")) {
+                        fileExecutables.add(filePath);
+                        //System.out.println("Executable [/usr/bin/file]: " + filePath);
+                    }
+                }
+            }
+            List <String> allExecutables = new ArrayList<String> ();
+            allExecutables.addAll(fileExecutables);
+            for(String s : executableList) {
+                    if(!allExecutables.contains(s)) {
+                        //System.out.println("Executable [ interpreter ]: " + s);
+                        allExecutables.add(s);
+                    }
+                }
+            chmod(allExecutables);
+        }
+    }
+
+    private void chmod(List <String> executables) {
+        if(executables.isEmpty()) {
+            return ;
+        }
+        if(System.getProperty("java.version").startsWith("1.5")) {
+            // Find chmod
+            File chmod = new File("/bin/chmod"); // NOI18N
+            if (!chmod.isFile()) {
+                chmod = new File("/usr/bin/chmod"); // NOI18N
+            }
+            if (chmod.isFile()) {
+                List <String> commands = new ArrayList<String>(executables.size() + 2);
+                commands.add(chmod.getAbsolutePath());
+                commands.add("a+x"); // NOI18N
+                commands.addAll(executables);
+                try {
+                    System.out.println("Executing command : " + commands);
+                    new ProcessBuilder(commands).start().waitFor();
+                } catch (Exception e) {
+                    e.printStackTrace();
+                }
+            }
+        } else {
+            // Determine if java.io.File.setExecutable method is supported
+            try {
+                Method setExecutableMethod = File.class.getMethod("setExecutable", new Class[] {Boolean.class, Boolean.class});
+                for(String s : executables) {
+                    setExecutableMethod.invoke(new File(s), true, false);
+                }
+            } catch (Exception e) {
+                e.printStackTrace();
+            }
+        }
+    }
+
+    private String readCommandOutput(List<String> command) {
+        ProcessBuilder builder = new ProcessBuilder(command);
+        boolean doRun = true;
+        StringBuilder sb = new StringBuilder();
+        byte[] bytes = new byte[8192];
+        int c = 0;
+
+        try {
+            Process process = builder.start();
+            while (doRun) {
+                try {
+                    Thread.sleep(20);
+                } catch (InterruptedException e) {
+                }
+                try {
+                    process.exitValue();
+                    doRun = false;
+                } catch (IllegalThreadStateException e) {
+                    ; // do nothing - the process is still running
+                }
+                InputStream is = process.getInputStream();
+                while ((c = is.read(bytes)) != -1) {
+                    sb.append(new String(bytes, 0, c));
+                }
+            }
+            return sb.toString();
+        } catch (IOException e) {
+            e.printStackTrace();
+            return new String();
+        }
+    }
     
      /** Quotes string correctly, eg. removes all quotes from the string and adds 
       * just one at the start and
@@ -564,8 +670,10 @@
      * @param progressVal The current progress bar value.  If this is
      *          negative, we don't want to update the progress bar.
      */
-    private long copyStreams( InputStream src, OutputStream dest,
-                               long progressVal ) throws java.io.IOException {
+     private long copyStreams( InputStream src, File destFile,
+                               long progressVal, List <String> list, List <String> executableList ) throws java.io.IOException {
+        OutputStream dest = new FileOutputStream(destFile);
+        list.add(destFile.getAbsolutePath());
 
         BufferedInputStream bsrc = new BufferedInputStream( src );
         BufferedOutputStream bdest = new BufferedOutputStream( dest );
@@ -574,10 +682,32 @@
 
         int c;
         byte [] bytes = new byte [8192];
-
+        boolean read = false;
         try {
             while( ( c = bsrc.read(bytes) ) != -1 ) {
                 bdest.write(bytes, 0, c);
+                if (!read) {
+                    read = true;
+                    if (c >= 4) { // length of ELF header and min length of "#!/X" string
+                        if (bytes[0] == '\177' &&
+                                bytes[1] == 'E' &&
+                                bytes[2] == 'L' &&
+                                bytes[3] == 'F') {
+                            executableList.add(destFile.getAbsolutePath());
+                        } else if (bytes[0] == '#' && bytes[1] == '!') {
+                            String s = new String(bytes, 0, c);
+                            String[] array = s.split("(?:\r\n|\n|\r)");
+
+                            if (array.length > 0) {
+                                //read the first line only
+                                //allow lines like "#! /bin/sh"
+                                if (array[0].replaceAll("#!(\\s)+/", "#!/").startsWith("#!/")) {
+                                    executableList.add(destFile.getAbsolutePath());
+                                }
+                            }
+                        }
+                    }
+                }
                 count+=c;
                 if ( count > 8500 ) {
                     if (progressVal >= 0) {