diff -r 0e23f9a2fdf6 j2eeserver/src/org/netbeans/modules/j2ee/deployment/devmodules/api/J2eeModule.java
--- a/j2eeserver/src/org/netbeans/modules/j2ee/deployment/devmodules/api/J2eeModule.java	Thu Nov 29 14:11:09 2012 +0100
+++ b/j2eeserver/src/org/netbeans/modules/j2ee/deployment/devmodules/api/J2eeModule.java	Thu Nov 29 15:08:19 2012 +0100
@@ -352,6 +352,12 @@
 
     }
 
+    public interface RootedEntry2 extends RootedEntry {
+
+        boolean isDirectoryDeployIgnored();
+        
+    }
+
     public static final class Type {
 
         public static final Type WAR = new Type(ModuleType.WAR);
diff -r 0e23f9a2fdf6 j2eeserver/src/org/netbeans/modules/j2ee/deployment/impl/InitialServerFileDistributor.java
--- a/j2eeserver/src/org/netbeans/modules/j2ee/deployment/impl/InitialServerFileDistributor.java	Thu Nov 29 14:11:09 2012 +0100
+++ b/j2eeserver/src/org/netbeans/modules/j2ee/deployment/impl/InitialServerFileDistributor.java	Thu Nov 29 15:08:19 2012 +0100
@@ -206,7 +206,8 @@
                     J2eeModule.RootedEntry entry = rootedEntries.next();
                     String relativePath = entry.getRelativePath();
                     FileObject sourceFO = entry.getFileObject();
-                    if (sourceFO.isData() && isArchiveInRootDir(root, sourceFO)) {
+                    if ((entry instanceof J2eeModule.RootedEntry2)
+                            && ((J2eeModule.RootedEntry2) entry).isDirectoryDeployIgnored()) {
                         continue;
                     }
                     FileObject destFolder = ServerFileDistributor.findOrCreateParentFolder(destRoot, relativePath);
@@ -228,13 +229,6 @@
         }
     }
 
-    private boolean isArchiveInRootDir(FileObject root, FileObject sourceFO) {
-        if (sourceFO.getParent().equals(root) && ("jar".equals(sourceFO.getExt()) || "war".equals(sourceFO.getExt()))) {
-            return true;
-        }
-        return false;
-    }
-
     //ServerProgress methods
     private void setStatusDistributeRunning(String message) {
         notify(createRunningProgressEvent(CommandType.DISTRIBUTE, message));