Merge branch 'stable-5.0'

* stable-5.0:
  Silence API warning for new ObjectIdSerializer introduced in 4.11.1
  Ignore API warnings
  Fix photon target platform to use photon version of org.eclipse.osgi
  Update Photon orbit repository to R20180606145124
  Suppress warning for trying to delete non-empty directory
  Fix fetching with duplicate ref updates
  Fetch(Process): should tolerate duplicate refspecs
  FetchCommandTest: test add/update/delete fetch

Change-Id: I9e7fa37b100a7ea3cbe4104802d36c6f38df9e08
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>

3 files changed, 34 insertions, 25 deletions

diff --git a/org.eclipse.jgit/.settings/.api_filters b/org.eclipse.jgit/.settings/.api_filters
index b7b49bc658..9f4b761495 100644
--- a/org.eclipse.jgit/.settings/.api_filters
+++ b/org.eclipse.jgit/.settings/.api_filters
@@ -7,22 +7,6 @@
             </message_arguments>
         </filter>
     </resource>
-    <resource path="src/org/eclipse/jgit/lib/ObjectIdSerializer.java" type="org.eclipse.jgit.lib.ObjectIdSerializer">
-        <filter id="1141899266">
-            <message_arguments>
-                <message_argument value="4.11"/>
-                <message_argument value="5.0"/>
-                <message_argument value="readWithoutMarker(InputStream)"/>
-            </message_arguments>
-        </filter>
-        <filter id="1141899266">
-            <message_arguments>
-                <message_argument value="4.11"/>
-                <message_argument value="5.0"/>
-                <message_argument value="writeWithoutMarker(OutputStream, AnyObjectId)"/>
-            </message_arguments>
-        </filter>
-    </resource>
     <resource path="src/org/eclipse/jgit/transport/GitProtocolConstants.java" type="org.eclipse.jgit.transport.GitProtocolConstants">
         <filter id="337768515">
             <message_arguments>
@@ -30,4 +14,4 @@
             </message_arguments>
         </filter>
     </resource>
-</component>
+</component>
\ No newline at end of file
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/RefDirectory.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/RefDirectory.java
index 7d2bd4897a..40c6de33fa 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/RefDirectory.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/RefDirectory.java
@@ -65,6 +65,7 @@ import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.io.InputStreamReader;
 import java.io.InterruptedIOException;
+import java.nio.file.DirectoryNotEmptyException;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.security.DigestInputStream;
@@ -1287,6 +1288,10 @@ public class RefDirectory extends RefDatabase {
 		for (int i = 0; i < depth; ++i) {
 			try {
 				Files.delete(dir.toPath());
+			} catch (DirectoryNotEmptyException e) {
+				// Don't log; normal case when there are other refs with the
+				// same prefix
+				break;
 			} catch (IOException e) {
 				LOG.warn("Unable to remove path {}", dir, e); //$NON-NLS-1$
 				break;
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/FetchProcess.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/FetchProcess.java
index ff183c8974..c43ab18c35 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/FetchProcess.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/FetchProcess.java
@@ -203,12 +203,10 @@ class FetchProcess {
 				((BatchingProgressMonitor) monitor).setDelayStart(
 						250, TimeUnit.MILLISECONDS);
 			}
-			if (transport.isRemoveDeletedRefs())
+			if (transport.isRemoveDeletedRefs()) {
 				deleteStaleTrackingRefs(result, batch);
-			for (TrackingRefUpdate u : localUpdates) {
-				result.add(u);
-				batch.addCommand(u.asReceiveCommand());
 			}
+			addUpdateBatchCommands(result, batch);
 			for (ReceiveCommand cmd : batch.getCommands()) {
 				cmd.updateType(walk);
 				if (cmd.getType() == UPDATE_NONFASTFORWARD
@@ -221,8 +219,11 @@ class FetchProcess {
 					if (cmd.getResult() == NOT_ATTEMPTED)
 						cmd.setResult(OK);
 				}
-			} else
+			} else {
 				batch.execute(walk, monitor);
+			}
+		} catch (TransportException e) {
+			throw e;
 		} catch (IOException err) {
 			throw new TransportException(MessageFormat.format(
 					JGitText.get().failureUpdatingTrackingRef,
@@ -239,6 +240,23 @@ class FetchProcess {
 		}
 	}
 
+	private void addUpdateBatchCommands(FetchResult result,
+			BatchRefUpdate batch) throws TransportException {
+		Map<String, ObjectId> refs = new HashMap<>();
+		for (TrackingRefUpdate u : localUpdates) {
+			// Try to skip duplicates if they'd update to the same object ID
+			ObjectId existing = refs.get(u.getLocalName());
+			if (existing == null) {
+				refs.put(u.getLocalName(), u.getNewObjectId());
+				result.add(u);
+				batch.addCommand(u.asReceiveCommand());
+			} else if (!existing.equals(u.getNewObjectId())) {
+				throw new TransportException(MessageFormat
+						.format(JGitText.get().duplicateRef, u.getLocalName()));
+			}
+		}
+	}
+
 	private void fetchObjects(ProgressMonitor monitor)
 			throws TransportException {
 		try {
@@ -479,15 +497,17 @@ class FetchProcess {
 
 	private void deleteStaleTrackingRefs(FetchResult result,
 			BatchRefUpdate batch) throws IOException {
+		Set<Ref> processed = new HashSet<>();
 		for (Ref ref : localRefs().values()) {
 			if (ref.isSymbolic()) {
 				continue;
 			}
-			final String refname = ref.getName();
+			String refname = ref.getName();
 			for (RefSpec spec : toFetch) {
 				if (spec.matchDestination(refname)) {
-					final RefSpec s = spec.expandFromDestination(refname);
-					if (result.getAdvertisedRef(s.getSource()) == null) {
+					RefSpec s = spec.expandFromDestination(refname);
+					if (result.getAdvertisedRef(s.getSource()) == null
+							&& processed.add(ref)) {
 						deleteTrackingRef(result, batch, s, ref);
 					}
 				}