Index: server/src/etc/conf/default/bootstrap-beans.xml
===================================================================
--- server/src/etc/conf/default/bootstrap-beans.xml	(revision 70412)
+++ server/src/etc/conf/default/bootstrap-beans.xml	(working copy)
@@ -358,5 +358,7 @@
       <property name="profileService"><inject bean="ProfileService"/></property>
       <property name="scanPeriod">5000</property>
       <property name="scanThreadName">HDScanner</property>
+      <!-- Fix for JBAS-5209. Use a filter to ignore files that are filtered from deployment -->
+      <property name="filterInstance"><inject bean="DeploymentFilter"/></property>
    </bean>
 </deployment>
Index: system/src/main/org/jboss/system/server/profileservice/hotdeploy/HDScanner.java
===================================================================
--- system/src/main/org/jboss/system/server/profileservice/hotdeploy/HDScanner.java	(revision 70412)
+++ system/src/main/org/jboss/system/server/profileservice/hotdeploy/HDScanner.java	(working copy)
@@ -38,6 +38,8 @@
 import org.jboss.profileservice.spi.ModificationInfo;
 import org.jboss.profileservice.spi.Profile;
 import org.jboss.profileservice.spi.ProfileService;
+import org.jboss.virtual.VirtualFile;
+import org.jboss.virtual.VirtualFileFilter;
 
 /**
  * A DeploymentScanner built on the ProfileService and MainDeployer. This
@@ -76,6 +78,9 @@
    private long scanPeriod = 5000;
    /** The number of scans that have been done */
    private int scanCount;
+   
+   /** Filter for scanned directories */
+   private VirtualFileFilter filter;   
 
    // Constructor ---------------------------------------------------
    
@@ -135,6 +140,27 @@
    {
       this.scanThreadName = scanThreadName;
    }
+   
+   /**
+    * Set the filter instance
+    * 
+    * @param filter ther filter
+    */
+   public void setFilterInstance(VirtualFileFilter filter)
+   {
+      this.filter = filter;
+   }
+   
+   /**
+    * Get the filter instance
+    * 
+    * @return the filter
+    */
+   public VirtualFileFilter getFilterInstance()
+   {
+      return filter;
+   }
+   
 
    /* (non-Javadoc)
     * @see org.jboss.deployment.scanner.VFSDeploymentScanner#getScanPeriod()
@@ -260,6 +286,16 @@
       Collection<ModificationInfo> modified = activeProfile.getModifiedDeployments();
       for(ModificationInfo info : modified)
       {
+    	  // Fix for JBAS-5209. Make sure that filtered files are NOT picked  
+    	  // up for deployment by the hot deployment scanner
+    	  VirtualFile virtualFile = info.getDeployment().getRoot();
+    	  if (this.filter != null && !this.filter.accepts(virtualFile)) {
+    		  if (trace) {
+    			  log.trace(info.getDeployment().getName() + " is filtered, hence not deploying");
+    		  }
+    		  continue;
+    	  }
+    	  
          VFSDeployment ctx = info.getDeployment();
          switch( info.getStatus() )
          {