Merge branch 'stable-5.13' into stable-6.0

* stable-5.13:
  Shortcut during git fetch for avoiding looping through all local refs
  FetchCommand: fix fetchSubmodules to work on a Ref to a blob
  Silence API warnings introduced by I466dcde6
  Allow the exclusions of refs prefixes from bitmap
  PackWriterBitmapPreparer: do not include annotated tags in bitmap
  BatchingProgressMonitor: avoid int overflow when computing percentage
  Speedup GC listing objects referenced from reflogs
  FileSnapshotTest: Add more MISSING_FILE coverage

Change-Id: I58ad4c210a5e7e5a1ba6b22315b04211c8909950

9 files changed, 110 insertions, 16 deletions

diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/FetchCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/FetchCommand.java
index 90c1515b06..7290d83df0 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/FetchCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/FetchCommand.java
@@ -140,6 +140,9 @@ public class FetchCommand extends TransportCommand<FetchCommand, FetchResult> {
 			if (fetchHead == null) {
 				return;
 			}
+			if (revWalk.parseAny(fetchHead).getType() == Constants.OBJ_BLOB) {
+				return;
+			}
 			walk.setTree(revWalk.parseTree(fetchHead));
 			while (walk.next()) {
 				try (Repository submoduleRepo = walk.getRepository()) {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/FileRepository.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/FileRepository.java
index 53a1cd6390..b37155717c 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/FileRepository.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/FileRepository.java
@@ -31,6 +31,7 @@ import java.util.Locale;
 import java.util.Objects;
 import java.util.Set;
 
+import org.eclipse.jgit.annotations.NonNull;
 import org.eclipse.jgit.annotations.Nullable;
 import org.eclipse.jgit.api.errors.JGitInternalException;
 import org.eclipse.jgit.attributes.AttributesNode;
@@ -530,6 +531,12 @@ public class FileRepository extends Repository {
 		return new ReflogReaderImpl(this, ref.getName());
 	}
 
+	@Override
+	public @NonNull ReflogReader getReflogReader(@NonNull Ref ref)
+			throws IOException {
+		return new ReflogReaderImpl(this, ref.getName());
+	}
+
 	/** {@inheritDoc} */
 	@Override
 	public AttributesNodeProvider createAttributesNodeProvider() {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/GC.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/GC.java
index ca4f7a21e3..8c0aca5153 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/GC.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/GC.java
@@ -794,6 +794,10 @@ public class GC {
 		Set<ObjectId> tagTargets = new HashSet<>();
 		Set<ObjectId> indexObjects = listNonHEADIndexObjects();
 
+		Set<ObjectId> refsToExcludeFromBitmap = repo.getRefDatabase()
+				.getRefsByPrefix(pconfig.getBitmapExcludedRefsPrefixes())
+				.stream().map(Ref::getObjectId).collect(Collectors.toSet());
+
 		for (Ref ref : refsBefore) {
 			checkCancelled();
 			nonHeads.addAll(listRefLogObjects(ref, 0));
@@ -838,7 +842,7 @@ public class GC {
 		Pack heads = null;
 		if (!allHeadsAndTags.isEmpty()) {
 			heads = writePack(allHeadsAndTags, PackWriter.NONE, allTags,
-					tagTargets, excluded);
+					refsToExcludeFromBitmap, tagTargets, excluded);
 			if (heads != null) {
 				ret.add(heads);
 				excluded.add(0, heads.getIndex());
@@ -846,13 +850,13 @@ public class GC {
 		}
 		if (!nonHeads.isEmpty()) {
 			Pack rest = writePack(nonHeads, allHeadsAndTags, PackWriter.NONE,
-					tagTargets, excluded);
+					PackWriter.NONE, tagTargets, excluded);
 			if (rest != null)
 				ret.add(rest);
 		}
 		if (!txnHeads.isEmpty()) {
 			Pack txn = writePack(txnHeads, PackWriter.NONE, PackWriter.NONE,
-					null, excluded);
+					PackWriter.NONE, null, excluded);
 			if (txn != null)
 				ret.add(txn);
 		}
@@ -1017,10 +1021,7 @@ public class GC {
 	 * @throws IOException
 	 */
 	private Set<ObjectId> listRefLogObjects(Ref ref, long minTime) throws IOException {
-		ReflogReader reflogReader = repo.getReflogReader(ref.getName());
-		if (reflogReader == null) {
-			return Collections.emptySet();
-		}
+		ReflogReader reflogReader = repo.getReflogReader(ref);
 		List<ReflogEntry> rlEntries = reflogReader
 				.getReverseEntries();
 		if (rlEntries == null || rlEntries.isEmpty())
@@ -1124,6 +1125,7 @@ public class GC {
 
 	private Pack writePack(@NonNull Set<? extends ObjectId> want,
 			@NonNull Set<? extends ObjectId> have, @NonNull Set<ObjectId> tags,
+			@NonNull Set<ObjectId> excludedRefsTips,
 			Set<ObjectId> tagTargets, List<ObjectIdSet> excludeObjects)
 			throws IOException {
 		checkCancelled();
@@ -1155,7 +1157,8 @@ public class GC {
 			if (excludeObjects != null)
 				for (ObjectIdSet idx : excludeObjects)
 					pw.excludeObjects(idx);
-			pw.preparePack(pm, want, have, PackWriter.NONE, tags);
+			pw.preparePack(pm, want, have, PackWriter.NONE,
+					union(tags, excludedRefsTips));
 			if (pw.getObjectCount() == 0)
 				return null;
 			checkCancelled();
@@ -1268,6 +1271,15 @@ public class GC {
 		}
 	}
 
+	private Set<? extends ObjectId> union(Set<ObjectId> tags,
+			Set<ObjectId> excludedRefsHeadsTips) {
+		HashSet<ObjectId> unionSet = new HashSet<>(
+				tags.size() + excludedRefsHeadsTips.size());
+		unionSet.addAll(tags);
+		unionSet.addAll(excludedRefsHeadsTips);
+		return unionSet;
+	}
+
 	private void checkCancelled() throws CancelledException {
 		if (pm.isCancelled() || Thread.currentThread().isInterrupted()) {
 			throw new CancelledException(JGitText.get().operationCanceled);
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/pack/PackWriterBitmapPreparer.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/pack/PackWriterBitmapPreparer.java
index 771d574bd4..5a18f1e567 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/pack/PackWriterBitmapPreparer.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/pack/PackWriterBitmapPreparer.java
@@ -408,6 +408,9 @@ class PackWriterBitmapPreparer {
 		List<RevCommit> newWantsByNewest = new ArrayList<>(want.size());
 		Set<RevCommit> newWants = new HashSet<>(want.size());
 		for (AnyObjectId objectId : want) {
+			if(excludeFromBitmapSelection.contains(objectId)) {
+				continue;
+			}
 			RevObject ro = rw.peel(rw.parseAny(objectId));
 			if (!(ro instanceof RevCommit) || reuse.contains(ro)
 					|| excludeFromBitmapSelection.contains(ro)) {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/BatchingProgressMonitor.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/BatchingProgressMonitor.java
index 2caefa4d97..49e295aed8 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/BatchingProgressMonitor.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/BatchingProgressMonitor.java
@@ -176,7 +176,7 @@ public abstract class BatchingProgressMonitor implements ProgressMonitor {
 				}
 			} else {
 				// Display once per second or when 1% is done.
-				int currPercent = lastWork * 100 / totalWork;
+				int currPercent = Math.round(lastWork * 100F / totalWork);
 				if (display) {
 					pm.onUpdate(taskName, lastWork, totalWork, currPercent);
 					output = true;
@@ -201,8 +201,8 @@ public abstract class BatchingProgressMonitor implements ProgressMonitor {
 				if (totalWork == UNKNOWN) {
 					pm.onEndTask(taskName, lastWork);
 				} else {
-					int pDone = lastWork * 100 / totalWork;
-					pm.onEndTask(taskName, lastWork, totalWork, pDone);
+					int currPercent = Math.round(lastWork * 100F / totalWork);
+					pm.onEndTask(taskName, lastWork, totalWork, currPercent);
 				}
 			}
 			if (timerFuture != null)
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/ConfigConstants.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/ConfigConstants.java
index 924328d8a6..6f76326bc9 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/ConfigConstants.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/ConfigConstants.java
@@ -621,6 +621,12 @@ public final class ConfigConstants {
 	public static final String CONFIG_KEY_BITMAP_EXCESSIVE_BRANCH_COUNT = "bitmapexcessivebranchcount";
 
 	/**
+	 * The "pack.bitmapExcludedRefsPrefixes" key
+	 * @since 5.13.2
+	 */
+	public static final String CONFIG_KEY_BITMAP_EXCLUDED_REFS_PREFIXES = "bitmapexcludedrefsprefixes";
+
+	/**
 	 * The "pack.bitmapInactiveBranchAgeInDays" key
 	 * @since 5.8
 	 */
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/Repository.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/Repository.java
index e594e528be..db2571c673 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/Repository.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/Repository.java
@@ -1695,6 +1695,22 @@ public abstract class Repository implements AutoCloseable {
 			throws IOException;
 
 	/**
+	 * Get the reflog reader. Subclasses should override this method and provide
+	 * a more efficient implementation.
+	 *
+	 * @param ref
+	 *            a Ref
+	 * @return a {@link org.eclipse.jgit.lib.ReflogReader} for the supplied ref,
+	 *         or {@code null} if the ref does not exist.
+	 * @throws IOException
+	 * @since 5.13.2
+	 */
+	public @Nullable ReflogReader getReflogReader(@NonNull	Ref ref)
+			throws IOException {
+		return getReflogReader(ref.getName());
+	}
+
+	/**
 	 * Return the information stored in the file $GIT_DIR/MERGE_MSG. In this
 	 * file operations triggering a merge will store a template for the commit
 	 * message of the merge commit.
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/storage/pack/PackConfig.java b/org.eclipse.jgit/src/org/eclipse/jgit/storage/pack/PackConfig.java
index 6aa8be642d..a10f6cf88a 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/storage/pack/PackConfig.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/storage/pack/PackConfig.java
@@ -16,6 +16,7 @@ import static org.eclipse.jgit.lib.ConfigConstants.CONFIG_KEY_BIGFILE_THRESHOLD;
 import static org.eclipse.jgit.lib.ConfigConstants.CONFIG_KEY_BITMAP_CONTIGUOUS_COMMIT_COUNT;
 import static org.eclipse.jgit.lib.ConfigConstants.CONFIG_KEY_BITMAP_DISTANT_COMMIT_SPAN;
 import static org.eclipse.jgit.lib.ConfigConstants.CONFIG_KEY_BITMAP_EXCESSIVE_BRANCH_COUNT;
+import static org.eclipse.jgit.lib.ConfigConstants.CONFIG_KEY_BITMAP_EXCLUDED_REFS_PREFIXES;
 import static org.eclipse.jgit.lib.ConfigConstants.CONFIG_KEY_BITMAP_INACTIVE_BRANCH_AGE_INDAYS;
 import static org.eclipse.jgit.lib.ConfigConstants.CONFIG_KEY_BITMAP_RECENT_COMMIT_COUNT;
 import static org.eclipse.jgit.lib.ConfigConstants.CONFIG_KEY_BUILD_BITMAPS;
@@ -226,6 +227,14 @@ public class PackConfig {
 	public static final int DEFAULT_BITMAP_INACTIVE_BRANCH_AGE_IN_DAYS = 90;
 
 	/**
+	 * Default refs prefixes excluded from the calculation of pack bitmaps.
+	 *
+	 * @see #setBitmapExcludedRefsPrefixes(String[])
+	 * @since 5.13.2
+	 */
+	public static final String[] DEFAULT_BITMAP_EXCLUDED_REFS_PREFIXES = new String[0];
+
+	/**
 	 * Default max time to spend during the search for reuse phase. This
 	 * optimization is disabled by default: {@value}
 	 *
@@ -285,6 +294,8 @@ public class PackConfig {
 
 	private int bitmapInactiveBranchAgeInDays = DEFAULT_BITMAP_INACTIVE_BRANCH_AGE_IN_DAYS;
 
+	private String[] bitmapExcludedRefsPrefixes = DEFAULT_BITMAP_EXCLUDED_REFS_PREFIXES;
+
 	private Duration searchForReuseTimeout = DEFAULT_SEARCH_FOR_REUSE_TIMEOUT;
 
 	private boolean cutDeltaChains;
@@ -1145,6 +1156,27 @@ public class PackConfig {
 	}
 
 	/**
+	 * Get the refs prefixes excluded from the Bitmap.
+	 *
+	 * @return the refs prefixes excluded from the Bitmap.
+	 * @since 5.13.2
+	 */
+	public String[] getBitmapExcludedRefsPrefixes() {
+		return bitmapExcludedRefsPrefixes;
+	}
+
+	/**
+	 * Set the refs prefixes excluded from the Bitmap.
+	 *
+	 * @param excludedRefsPrefixes
+	 *            the refs prefixes excluded from the Bitmap.
+	 * @since 5.13.2
+	 */
+	public void setBitmapExcludedRefsPrefixes(String[] excludedRefsPrefixes) {
+		bitmapExcludedRefsPrefixes = excludedRefsPrefixes;
+	}
+
+	/**
 	 * Set the max time to spend during the search for reuse phase.
 	 *
 	 * @param timeout
@@ -1220,6 +1252,12 @@ public class PackConfig {
 		setBitmapInactiveBranchAgeInDays(rc.getInt(CONFIG_PACK_SECTION,
 				CONFIG_KEY_BITMAP_INACTIVE_BRANCH_AGE_INDAYS,
 				getBitmapInactiveBranchAgeInDays()));
+		String[] excludedRefsPrefixesArray = rc.getStringList(CONFIG_PACK_SECTION,
+			null,
+			CONFIG_KEY_BITMAP_EXCLUDED_REFS_PREFIXES);
+		if(excludedRefsPrefixesArray.length > 0) {
+			setBitmapExcludedRefsPrefixes(excludedRefsPrefixesArray);
+		}
 		setSearchForReuseTimeout(Duration.ofSeconds(rc.getTimeUnit(
 				CONFIG_PACK_SECTION, null,
 				CONFIG_KEY_SEARCH_FOR_REUSE_TIMEOUT,
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 2b4deb32f0..1c1aa7b310 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/FetchProcess.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/FetchProcess.java
@@ -46,6 +46,7 @@ import org.eclipse.jgit.lib.ProgressMonitor;
 import org.eclipse.jgit.lib.Ref;
 import org.eclipse.jgit.lib.RefDatabase;
 import org.eclipse.jgit.revwalk.ObjectWalk;
+import org.eclipse.jgit.revwalk.RevObject;
 import org.eclipse.jgit.revwalk.RevWalk;
 import org.eclipse.jgit.util.StringUtils;
 
@@ -377,11 +378,19 @@ class FetchProcess {
 	private boolean askForIsComplete() throws TransportException {
 		try {
 			try (ObjectWalk ow = new ObjectWalk(transport.local)) {
-				for (ObjectId want : askFor.keySet())
-					ow.markStart(ow.parseAny(want));
-				for (Ref ref : localRefs().values())
-					ow.markUninteresting(ow.parseAny(ref.getObjectId()));
-				ow.checkConnectivity();
+				boolean hasCommitObject = false;
+				for (ObjectId want : askFor.keySet()) {
+					RevObject obj = ow.parseAny(want);
+					ow.markStart(obj);
+					hasCommitObject |= obj.getType() == Constants.OBJ_COMMIT;
+				}
+				// Checking connectivity makes sense on commits only
+				if (hasCommitObject) {
+					for (Ref ref : localRefs().values()) {
+						ow.markUninteresting(ow.parseAny(ref.getObjectId()));
+					}
+					ow.checkConnectivity();
+				}
 			}
 			return true;
 		} catch (MissingObjectException e) {