### Eclipse Workspace Patch 1.0
#P org.eclipse.jdt.core
Index: model/org/eclipse/jdt/internal/core/JavaModelManager.java
===================================================================
RCS file: /cvsroot/eclipse/org.eclipse.jdt.core/model/org/eclipse/jdt/internal/core/JavaModelManager.java,v
retrieving revision 1.408
diff -u -r1.408 JavaModelManager.java
--- model/org/eclipse/jdt/internal/core/JavaModelManager.java	1 Sep 2008 08:53:56 -0000	1.408
+++ model/org/eclipse/jdt/internal/core/JavaModelManager.java	2 Sep 2008 14:49:48 -0000
@@ -1069,6 +1069,8 @@
 						if (target instanceof File) {
 							long timestamp = DeltaProcessor.getTimeStamp((java.io.File)target);
 							externalTimeStamps.put(path, new Long(timestamp));
+						} else {
+							externalTimeStamps.put(path, DeltaProcessingState.MISSING_JAR);
 						}
 					}
 				}
Index: model/org/eclipse/jdt/internal/core/DeltaProcessor.java
===================================================================
RCS file: /cvsroot/eclipse/org.eclipse.jdt.core/model/org/eclipse/jdt/internal/core/DeltaProcessor.java,v
retrieving revision 1.326
diff -u -r1.326 DeltaProcessor.java
--- model/org/eclipse/jdt/internal/core/DeltaProcessor.java	27 Aug 2008 08:59:19 -0000	1.326
+++ model/org/eclipse/jdt/internal/core/DeltaProcessor.java	2 Sep 2008 14:49:47 -0000
@@ -864,7 +864,8 @@
 						Object targetLibrary = JavaModel.getTarget(entryPath, true);
 
 						if (targetLibrary == null){ // missing JAR
-							if (this.state.getExternalLibTimeStamps().remove(entryPath) != null /* file was known*/
+							Long oldTimestamp = (Long) this.state.getExternalLibTimeStamps().put(entryPath, DeltaProcessingState.MISSING_JAR);
+							if (oldTimestamp != null && oldTimestamp != DeltaProcessingState.MISSING_JAR/* file was known*/
 									&& this.state.roots.get(entryPath) != null /* and it was on the classpath*/) {
 								externalArchivesStatus.put(entryPath, EXTERNAL_JAR_REMOVED);
 								// the jar was physically removed: remove the index
@@ -878,11 +879,11 @@
 							// check timestamp to figure if JAR has changed in some way
 							Long oldTimestamp =(Long) this.state.getExternalLibTimeStamps().get(entryPath);
 							long newTimeStamp = getTimeStamp(externalFile);
-							if (oldTimestamp != null){
+							if (oldTimestamp != null && oldTimestamp != DeltaProcessingState.MISSING_JAR) {
 
 								if (newTimeStamp == 0){ // file doesn't exist
 									externalArchivesStatus.put(entryPath, EXTERNAL_JAR_REMOVED);
-									this.state.getExternalLibTimeStamps().remove(entryPath);
+									this.state.getExternalLibTimeStamps().put(entryPath, DeltaProcessingState.MISSING_JAR);
 									// remove the index
 									this.manager.indexManager.removeIndex(entryPath);
 
Index: model/org/eclipse/jdt/internal/core/DeltaProcessingState.java
===================================================================
RCS file: /cvsroot/eclipse/org.eclipse.jdt.core/model/org/eclipse/jdt/internal/core/DeltaProcessingState.java,v
retrieving revision 1.50
diff -u -r1.50 DeltaProcessingState.java
--- model/org/eclipse/jdt/internal/core/DeltaProcessingState.java	27 Jun 2008 16:03:51 -0000	1.50
+++ model/org/eclipse/jdt/internal/core/DeltaProcessingState.java	2 Sep 2008 14:49:47 -0000
@@ -30,6 +30,8 @@
  * Keep the global states used during Java element delta processing.
  */
 public class DeltaProcessingState implements IResourceChangeListener {
+	
+	public static final Long MISSING_JAR = new Long(-1);
 
 	/*
 	 * Collection of listeners for Java element deltas
@@ -449,7 +451,7 @@
 				while (size-- > 0) {
 					String key = in.readUTF();
 					long timestamp = in.readLong();
-					timeStamps.put(Path.fromPortableString(key), new Long(timestamp));
+					timeStamps.put(Path.fromPortableString(key), timestamp == -1 ? MISSING_JAR : new Long(timestamp));
 				}
 			} catch (IOException e) {
 				if (timestampsFile.exists())
#P org.eclipse.jdt.core.tests.model
Index: src/org/eclipse/jdt/core/tests/model/ClasspathTests.java
===================================================================
RCS file: /cvsroot/eclipse/org.eclipse.jdt.core.tests.model/src/org/eclipse/jdt/core/tests/model/ClasspathTests.java,v
retrieving revision 1.182
diff -u -r1.182 ClasspathTests.java
--- src/org/eclipse/jdt/core/tests/model/ClasspathTests.java	1 Sep 2008 14:46:52 -0000	1.182
+++ src/org/eclipse/jdt/core/tests/model/ClasspathTests.java	2 Sep 2008 14:49:50 -0000
@@ -2687,7 +2687,7 @@
  * Ensures that a marker is removed if adding an internal jar that is on the classpath in another project
  * (regression test for https://bugs.eclipse.org/bugs/show_bug.cgi?id=213723 )
  */
-public void testFixClasspath() throws CoreException {
+public void testFixClasspath1() throws CoreException {
 	try {
 		createProject("P1");
 		IJavaProject project = createJavaProject("P2", new String[0], new String[] {"/P1/lib.jar"}, "bin");
@@ -2703,6 +2703,25 @@
 		deleteProject("P2");
 	}
 }
+/*
+ * Ensures that a marker is removed if adding an external jar, restarting and refreshing
+ * (regression test for https://bugs.eclipse.org/bugs/show_bug.cgi?id=216446 )
+ */
+public void testFixClasspath2() throws CoreException {
+	try {
+		IJavaProject p = createJavaProject("P", new String[0], new String[] {getExternalResourcePath("externalLib.abc")}, "");
+		waitForAutoBuild(); // 1 marker
+		createExternalFile("externalLib.abc", "");
+		
+		simulateExitRestart();
+		refreshExternalArchives(p);
+		
+		assertMarkers("Unexpected markers", "", p);
+	} finally {
+		deleteExternalResource("externalLib.abc");
+		deleteProject("P");
+	}
+}
 /**
  * Test IJavaProject.hasClasspathCycle(IClasspathEntry[]).
  */