Reproducible with EE.  This is high-priority because basic EE functionality is 
broken.  Create an ejb and ejbmodule (or mount attached files) and use Export 
Jar action:

java.lang.NullPointerException
	at org.openide.filesystems.FileUtil.toFile(FileUtil.java:247)
	at org.openide.filesystems.FileUtil.fromFile(FileUtil.java:281)
	at org.netbeans.modules.jarpackager.JarCreator.recognizeFile
(JarCreator.java:679)
	at org.netbeans.modules.jarpackager.JarCreator.createJar
(JarCreator.java:147)
	at org.netbeans.modules.jarpackager.JarCreator.createJar
(JarCreator.java:106)
	at com.sun.forte4j.j2ee.packaging.PackagingUtil.writeJarFile
(PackagingUtil.java:263)
	at com.sun.forte4j.j2ee.ejbmodule.EJBModuleDataObject.writeEJBJar
(EJBModuleDataObject.java:2227)
	at 
com.sun.forte4j.j2ee.ejbmodule.actions.WriteEJBJarAction$1.computeClosure
(WriteEJBJarAction.java:82)
	at org.netbeans.modules.classclosure.ClosureCompiler$Group.start
(ClosureCompiler.java:93)
	at 
org.netbeans.core.compiler.CompilationEngineImpl$CompilerThread$GroupCompiler.ru
n(CompilationEngineImpl.java:257)

The cause is that in FileUtil.fromFile(), a recent code change caused "fo" to 
be referenced before it is tested for null:

>                 if (fileName.indexOf(rootName) == 0) {
>                     String res = fileName.substring(rootName.length()).replace
(File.separatorChar, '/');
>                     FileObject fo = fs.findResource(res);
>                     File       file2Fo = toFile(fo);
>                     if (fo != null && file2Fo != null &&
>                     file.equals(file2Fo.getCanonicalFile()))
>                         list.add(fo);
>                 }