Bug 525382 - [9] Project having multiple output folders throws CNFE
while running with JDK9

Change-Id: I2bc03f36e970a855f365c8d131061d36d7322d82
diff --git a/org.eclipse.jdt.launching/launching/org/eclipse/jdt/launching/JavaRuntime.java b/org.eclipse.jdt.launching/launching/org/eclipse/jdt/launching/JavaRuntime.java
index c0e1f5b..7472fdf 100644
--- a/org.eclipse.jdt.launching/launching/org/eclipse/jdt/launching/JavaRuntime.java
+++ b/org.eclipse.jdt.launching/launching/org/eclipse/jdt/launching/JavaRuntime.java
@@ -1525,7 +1525,10 @@
 						}
 						else {
 							IPackageFragmentRoot root = project.findPackageFragmentRoot(entry.getPath());
-							if (root != null && !root.getRawClasspathEntry().getPath().segment(0).contains("JRE_CONTAINER")) { //$NON-NLS-1$
+							if ( root == null) {
+								entries2.add(entry);
+							}
+							else if (root != null && !root.getRawClasspathEntry().getPath().segment(0).contains("JRE_CONTAINER")) { //$NON-NLS-1$
 								entries2.add(entry);
 							}
 						}