2 files changed, 35 insertions, 11 deletions

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 7d7b3ee0a0..2b4deb32f0 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/FetchProcess.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/FetchProcess.java
@@ -204,8 +204,13 @@ class FetchProcess {
 
 		BatchRefUpdate batch = transport.local.getRefDatabase()
 				.newBatchUpdate()
-				.setAllowNonFastForwards(true)
-				.setRefLogMessage("fetch", true); //$NON-NLS-1$
+				.setAllowNonFastForwards(true);
+
+		// Generate reflog only when fetching updates and not at the first clone
+		if (initialBranch == null) {
+			batch.setRefLogMessage("fetch", true); //$NON-NLS-1$
+		}
+
 		try (RevWalk walk = new RevWalk(transport.local)) {
 			walk.setRetainBody(false);
 			if (monitor instanceof BatchingProgressMonitor) {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/UploadPack.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/UploadPack.java
index 0a7eb17f05..6cb8fe43c0 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/UploadPack.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/UploadPack.java
@@ -39,6 +39,7 @@ import static org.eclipse.jgit.transport.GitProtocolConstants.VERSION_2_REQUEST;
 import static org.eclipse.jgit.util.RefMap.toRefMap;
 
 import java.io.ByteArrayOutputStream;
+import java.io.Closeable;
 import java.io.EOFException;
 import java.io.IOException;
 import java.io.InputStream;
@@ -105,7 +106,7 @@ import org.eclipse.jgit.util.io.TimeoutOutputStream;
 /**
  * Implements the server side of a fetch connection, transmitting objects.
  */
-public class UploadPack {
+public class UploadPack implements Closeable {
 	/** Policy the server uses to validate client requests */
 	public enum RequestPolicy {
 		/** Client may only ask for objects the server advertised a reference for. */
@@ -733,6 +734,17 @@ public class UploadPack {
 				&& clientRequestedV2;
 	}
 
+	@Override
+	public void close() {
+		if (timer != null) {
+			try {
+				timer.terminate();
+			} finally {
+				timer = null;
+			}
+		}
+	}
+
 	/**
 	 * Execute the upload task on the socket.
 	 *
@@ -780,6 +792,8 @@ public class UploadPack {
 				throw new UploadPackInternalServerErrorException(err);
 			}
 			throw err;
+		} finally {
+			close();
 		}
 	}
 
@@ -789,6 +803,10 @@ public class UploadPack {
 	 * <p>
 	 * If the client passed extra parameters (e.g., "version=2") through a side
 	 * channel, the caller must call setExtraParameters first to supply them.
+	 * Callers of this method should call {@link #close()} to terminate the
+	 * internal interrupt timer thread. If the caller fails to terminate the
+	 * thread, it will (eventually) terminate itself when the InterruptTimer
+	 * instance is garbage collected.
 	 *
 	 * @param input
 	 *            raw input to read client commands from. Caller must ensure the
@@ -845,13 +863,6 @@ public class UploadPack {
 		} finally {
 			msgOut = NullOutputStream.INSTANCE;
 			walk.close();
-			if (timer != null) {
-				try {
-					timer.terminate();
-				} finally {
-					timer = null;
-				}
-			}
 		}
 	}
 
@@ -1998,12 +2009,16 @@ public class UploadPack {
 			throws IOException {
 
 		ObjectReader reader = up.getRevWalk().getObjectReader();
+		Set<ObjectId> directlyVisibleObjects = refIdSet(visibleRefs);
+		List<ObjectId> nonTipWants = notAdvertisedWants.stream()
+				.filter(not(directlyVisibleObjects::contains))
+				.collect(Collectors.toList());
 
 		try (RevWalk walk = new RevWalk(reader)) {
 			walk.setRetainBody(false);
 			// Missing "wants" throw exception here
 			List<RevObject> wantsAsObjs = objectIdsToRevObjects(walk,
-					notAdvertisedWants);
+					nonTipWants);
 			List<RevCommit> wantsAsCommits = wantsAsObjs.stream()
 					.filter(obj -> obj instanceof RevCommit)
 					.map(obj -> (RevCommit) obj)
@@ -2063,6 +2078,10 @@ public class UploadPack {
 		}
 	}
 
+	private static <T> Predicate<T> not(Predicate<T> t) {
+	    return t.negate();
+	}
+
 	static Stream<Ref> importantRefsFirst(
 			Collection<Ref> visibleRefs) {
 		Predicate<Ref> startsWithRefsHeads = ref -> ref.getName()