Merge branch 'master' into stable-5.9

* master:
  SshdSession: close channel gracefully
  jgit: Add DfsBundleWriter
  Prepare 5.10.0-SNAPSHOT builds
  ResolveMerger: do not content-merge gitlinks on del/mod conflicts
  ResolveMerger: Adding test cases for GITLINK deletion
  ResolveMerger: choose OURS on gitlink when ignoreConflicts
  ResolveMerger: improving content merge readability
  ResolveMerger: extracting createGitLinksMergeResult method
  ResolveMerger: Adding test cases for GITLINK merge

Back out the version change to 5.10.0-SNAPSHOT which was done on master
already.

Change-Id: I1a6b1f0b8f5773be47823d74f593d13b16a601d5
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>

4 files changed, 179 insertions, 58 deletions

diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsBundleWriter.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsBundleWriter.java
new file mode 100644
index 0000000000..736f381d78
--- /dev/null
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsBundleWriter.java
@@ -0,0 +1,52 @@
+/*
+ * Copyright (c) 2020, Google LLC  and others
+ *
+ * This program and the accompanying materials are made available under the
+ * terms of the Eclipse Distribution License v. 1.0 which is available at
+ * http://www.eclipse.org/org/documents/edl-v10.php.
+ *
+ * SPDX-License-Identifier: BSD-3-Clause
+ */
+package org.eclipse.jgit.internal.storage.dfs;
+
+import java.io.IOException;
+import java.io.OutputStream;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.eclipse.jgit.internal.storage.pack.CachedPack;
+import org.eclipse.jgit.lib.ProgressMonitor;
+import org.eclipse.jgit.transport.BundleWriter;
+
+/** Writes {@link DfsRepository} to a Git bundle. */
+public class DfsBundleWriter {
+	/**
+	 * Writes the entire {@link DfsRepository} to a Git bundle.
+	 * <p>
+	 * This method try to avoid traversing the pack files as much as possible
+	 * and dumps all objects as-is to a Git bundle.
+	 *
+	 * @param pm
+	 *            progress monitor
+	 * @param os
+	 *            Git bundle output
+	 * @param db
+	 *            repository
+	 * @throws IOException
+	 *             thrown if the output stream throws one.
+	 */
+	public static void writeEntireRepositoryAsBundle(ProgressMonitor pm,
+			OutputStream os, DfsRepository db) throws IOException {
+		BundleWriter bw = new BundleWriter(db);
+		db.getRefDatabase().getRefs().forEach(bw::include);
+		List<CachedPack> packs = new ArrayList<>();
+		for (DfsPackFile p : db.getObjectDatabase().getPacks()) {
+			packs.add(new DfsCachedPack(p));
+		}
+		bw.addObjectsAsIs(packs);
+		bw.writeBundle(pm, os);
+	}
+
+	private DfsBundleWriter() {
+	}
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/pack/PackWriter.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/pack/PackWriter.java
index 9e409490fa..3e4b5df6aa 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/pack/PackWriter.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/pack/PackWriter.java
@@ -756,6 +756,19 @@ public class PackWriter implements AutoCloseable {
 
 	/**
 	 * Prepare the list of objects to be written to the pack stream.
+	 *
+	 * <p>
+	 * PackWriter will concat and write out the specified packs as-is.
+	 *
+	 * @param c
+	 *            cached packs to be written.
+	 */
+	public void preparePack(Collection<? extends CachedPack> c) {
+		cachedPacks.addAll(c);
+	}
+
+	/**
+	 * Prepare the list of objects to be written to the pack stream.
 	 * <p>
 	 * Basing on these 2 sets, another set of objects to put in a pack file is
 	 * created: this set consists of all objects reachable (ancestors) from
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/merge/ResolveMerger.java b/org.eclipse.jgit/src/org/eclipse/jgit/merge/ResolveMerger.java
index 506d333120..6c217fdf25 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/merge/ResolveMerger.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/merge/ResolveMerger.java
@@ -588,7 +588,8 @@ public class ResolveMerger extends ThreeWayMerger {
 		final int modeO = tw.getRawMode(T_OURS);
 		final int modeT = tw.getRawMode(T_THEIRS);
 		final int modeB = tw.getRawMode(T_BASE);
-
+		boolean gitLinkMerging = isGitLink(modeO) || isGitLink(modeT)
+				|| isGitLink(modeB);
 		if (modeO == 0 && modeT == 0 && modeB == 0)
 			// File is either untracked or new, staged but uncommitted
 			return true;
@@ -737,31 +738,28 @@ public class ResolveMerger extends ThreeWayMerger {
 				return false;
 			}
 
-			boolean gitlinkConflict = isGitLink(modeO) || isGitLink(modeT);
-			// Don't attempt to resolve submodule link conflicts
-			if (gitlinkConflict || !attributes.canBeContentMerged()) {
+			if (gitLinkMerging && ignoreConflicts) {
+				// Always select 'ours' in case of GITLINK merge failures so
+				// a caller can use virtual commit.
+				add(tw.getRawPath(), ours, DirCacheEntry.STAGE_0, EPOCH, 0);
+				return true;
+			} else if (gitLinkMerging) {
+				add(tw.getRawPath(), base, DirCacheEntry.STAGE_1, EPOCH, 0);
+				add(tw.getRawPath(), ours, DirCacheEntry.STAGE_2, EPOCH, 0);
+				add(tw.getRawPath(), theirs, DirCacheEntry.STAGE_3, EPOCH, 0);
+				MergeResult<SubmoduleConflict> result = createGitLinksMergeResult(
+						base, ours, theirs);
+				result.setContainsConflicts(true);
+				mergeResults.put(tw.getPathString(), result);
+				unmergedPaths.add(tw.getPathString());
+				return true;
+			} else if (!attributes.canBeContentMerged()) {
 				add(tw.getRawPath(), base, DirCacheEntry.STAGE_1, EPOCH, 0);
 				add(tw.getRawPath(), ours, DirCacheEntry.STAGE_2, EPOCH, 0);
 				add(tw.getRawPath(), theirs, DirCacheEntry.STAGE_3, EPOCH, 0);
 
-				if (gitlinkConflict) {
-					MergeResult<SubmoduleConflict> result = new MergeResult<>(
-							Arrays.asList(
-									new SubmoduleConflict(base == null ? null
-											: base.getEntryObjectId()),
-									new SubmoduleConflict(ours == null ? null
-											: ours.getEntryObjectId()),
-									new SubmoduleConflict(theirs == null ? null
-											: theirs.getEntryObjectId())));
-					result.setContainsConflicts(true);
-					mergeResults.put(tw.getPathString(), result);
-					if (!ignoreConflicts) {
-						unmergedPaths.add(tw.getPathString());
-					}
-				} else {
-					// attribute merge issues are conflicts but not failures
-					unmergedPaths.add(tw.getPathString());
-				}
+				// attribute merge issues are conflicts but not failures
+				unmergedPaths.add(tw.getPathString());
 				return true;
 			}
 
@@ -786,45 +784,73 @@ public class ResolveMerger extends ThreeWayMerger {
 			// OURS or THEIRS has been deleted
 			if (((modeO != 0 && !tw.idEqual(T_BASE, T_OURS)) || (modeT != 0 && !tw
 					.idEqual(T_BASE, T_THEIRS)))) {
-				MergeResult<RawText> result = contentMerge(base, ours, theirs,
-						attributes);
-
-				if (ignoreConflicts) {
-					// In case a conflict is detected the working tree file is
-					// again filled with new content (containing conflict
-					// markers). But also stage 0 of the index is filled with
-					// that content.
-					result.setContainsConflicts(false);
-					updateIndex(base, ours, theirs, result, attributes);
-				} else {
+				if (gitLinkMerging && ignoreConflicts) {
+					add(tw.getRawPath(), ours, DirCacheEntry.STAGE_0, EPOCH, 0);
+				} else if (gitLinkMerging) {
 					add(tw.getRawPath(), base, DirCacheEntry.STAGE_1, EPOCH, 0);
 					add(tw.getRawPath(), ours, DirCacheEntry.STAGE_2, EPOCH, 0);
-					DirCacheEntry e = add(tw.getRawPath(), theirs,
-							DirCacheEntry.STAGE_3, EPOCH, 0);
-
-					// OURS was deleted checkout THEIRS
-					if (modeO == 0) {
-						// Check worktree before checking out THEIRS
-						if (isWorktreeDirty(work, ourDce)) {
-							return false;
-						}
-						if (nonTree(modeT)) {
-							if (e != null) {
-								addToCheckout(tw.getPathString(), e, attributes);
+					add(tw.getRawPath(), theirs, DirCacheEntry.STAGE_3, EPOCH, 0);
+					MergeResult<SubmoduleConflict> result = createGitLinksMergeResult(
+							base, ours, theirs);
+					result.setContainsConflicts(true);
+					mergeResults.put(tw.getPathString(), result);
+					unmergedPaths.add(tw.getPathString());
+				} else {
+					MergeResult<RawText> result = contentMerge(base, ours,
+							theirs, attributes);
+
+					if (ignoreConflicts) {
+						// In case a conflict is detected the working tree file
+						// is again filled with new content (containing conflict
+						// markers). But also stage 0 of the index is filled
+						// with that content.
+						result.setContainsConflicts(false);
+						updateIndex(base, ours, theirs, result, attributes);
+					} else {
+						add(tw.getRawPath(), base, DirCacheEntry.STAGE_1, EPOCH,
+								0);
+						add(tw.getRawPath(), ours, DirCacheEntry.STAGE_2, EPOCH,
+								0);
+						DirCacheEntry e = add(tw.getRawPath(), theirs,
+								DirCacheEntry.STAGE_3, EPOCH, 0);
+
+						// OURS was deleted checkout THEIRS
+						if (modeO == 0) {
+							// Check worktree before checking out THEIRS
+							if (isWorktreeDirty(work, ourDce)) {
+								return false;
+							}
+							if (nonTree(modeT)) {
+								if (e != null) {
+									addToCheckout(tw.getPathString(), e,
+											attributes);
+								}
 							}
 						}
-					}
 
-					unmergedPaths.add(tw.getPathString());
+						unmergedPaths.add(tw.getPathString());
 
-					// generate a MergeResult for the deleted file
-					mergeResults.put(tw.getPathString(), result);
+						// generate a MergeResult for the deleted file
+						mergeResults.put(tw.getPathString(), result);
+					}
 				}
 			}
 		}
 		return true;
 	}
 
+	private static MergeResult<SubmoduleConflict> createGitLinksMergeResult(
+			CanonicalTreeParser base, CanonicalTreeParser ours,
+			CanonicalTreeParser theirs) {
+		return new MergeResult<>(Arrays.asList(
+				new SubmoduleConflict(
+						base == null ? null : base.getEntryObjectId()),
+				new SubmoduleConflict(
+						ours == null ? null : ours.getEntryObjectId()),
+				new SubmoduleConflict(
+						theirs == null ? null : theirs.getEntryObjectId())));
+	}
+
 	/**
 	 * Does the content merge. The three texts base, ours and theirs are
 	 * specified with {@link CanonicalTreeParser}. If any of the parsers is
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/BundleWriter.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/BundleWriter.java
index 57eed3ad2a..e1aa9d72fb 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/BundleWriter.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/BundleWriter.java
@@ -17,12 +17,16 @@ import java.io.OutputStream;
 import java.io.OutputStreamWriter;
 import java.io.Writer;
 import java.text.MessageFormat;
+import java.util.ArrayList;
+import java.util.Collection;
 import java.util.HashSet;
+import java.util.List;
 import java.util.Map;
 import java.util.Set;
 import java.util.TreeMap;
 
 import org.eclipse.jgit.internal.JGitText;
+import org.eclipse.jgit.internal.storage.pack.CachedPack;
 import org.eclipse.jgit.internal.storage.pack.PackWriter;
 import org.eclipse.jgit.lib.AnyObjectId;
 import org.eclipse.jgit.lib.Constants;
@@ -62,6 +66,8 @@ public class BundleWriter {
 
 	private final Set<ObjectId> tagTargets;
 
+	private final List<CachedPack> cachedPacks = new ArrayList<>();
+
 	private PackConfig packConfig;
 
 	private ObjectCountCallback callback;
@@ -150,6 +156,25 @@ public class BundleWriter {
 	}
 
 	/**
+	 * Add objects to the bundle file.
+	 *
+	 * <p>
+	 * When this method is used, object traversal is disabled and specified pack
+	 * files are directly saved to the Git bundle file.
+	 *
+	 * <p>
+	 * Unlike {@link #include}, this doesn't affect the refs. Even if the
+	 * objects are not reachable from any ref, they will be included in the
+	 * bundle file.
+	 *
+	 * @param c
+	 *            pack to include
+	 */
+	public void addObjectsAsIs(Collection<? extends CachedPack> c) {
+		cachedPacks.addAll(c);
+	}
+
+	/**
 	 * Assume a commit is available on the recipient's side.
 	 * <p>
 	 * In order to fetch from a bundle the recipient must have any assumed
@@ -187,19 +212,24 @@ public class BundleWriter {
 		try (PackWriter packWriter = newPackWriter()) {
 			packWriter.setObjectCountCallback(callback);
 
-			final HashSet<ObjectId> inc = new HashSet<>();
-			final HashSet<ObjectId> exc = new HashSet<>();
-			inc.addAll(include.values());
-			for (RevCommit r : assume)
-				exc.add(r.getId());
 			packWriter.setIndexDisabled(true);
 			packWriter.setDeltaBaseAsOffset(true);
-			packWriter.setThin(!exc.isEmpty());
 			packWriter.setReuseValidatingObjects(false);
-			if (exc.isEmpty()) {
-				packWriter.setTagTargets(tagTargets);
+			if (cachedPacks.isEmpty()) {
+				HashSet<ObjectId> inc = new HashSet<>();
+				HashSet<ObjectId> exc = new HashSet<>();
+				inc.addAll(include.values());
+				for (RevCommit r : assume) {
+					exc.add(r.getId());
+				}
+				if (exc.isEmpty()) {
+					packWriter.setTagTargets(tagTargets);
+				}
+				packWriter.setThin(!exc.isEmpty());
+				packWriter.preparePack(monitor, inc, exc);
+			} else {
+				packWriter.preparePack(cachedPacks);
 			}
-			packWriter.preparePack(monitor, inc, exc);
 
 			final Writer w = new OutputStreamWriter(os, UTF_8);
 			w.write(TransportBundle.V2_BUNDLE_SIGNATURE);