Merge branch 'stable-5.12' into stable-5.13

* stable-5.12:
  Fix missing peel-part in lsRefsV2 for loose annotated tags
  Fix RevWalk.getMergedInto() ignores annotated tags
  Optimize RevWalk.getMergedInto()
  reftable: drop code for truncated reads
  reftable: pass on invalid object ID in conversion
  Update eclipse-jarsigner-plugin to 1.3.2
  Fix running benchmarks from bazel
  Update eclipse-jarsigner-plugin to 1.3.2

Change-Id: Ie5da8d2d07f39ab5aaeca560040637635d4eb04c

5 files changed, 177 insertions, 13 deletions

diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/FileReftableTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/FileReftableTest.java
index 15c9109ca0..32342e3563 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/FileReftableTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/FileReftableTest.java
@@ -25,7 +25,9 @@ import static org.junit.Assert.assertTrue;
 import static org.junit.Assert.fail;
 
 import java.io.File;
+import java.io.FileOutputStream;
 import java.io.IOException;
+import java.io.OutputStream;
 import java.security.SecureRandom;
 import java.util.ArrayList;
 import java.util.Collection;
@@ -133,20 +135,21 @@ public class FileReftableTest extends SampleDataRepositoryTestCase {
 		assertTrue(db.getRefDatabase().hasFastTipsWithSha1());
 	}
 
+
 	@Test
-	public void testConvertToRefdir() throws Exception {
+	public void testConvertBrokenObjectId() throws Exception {
 		db.convertToPackedRefs(false, false);
-		assertTrue(db.getRefDatabase() instanceof RefDirectory);
-		Ref h = db.exactRef("HEAD");
-		assertTrue(h.isSymbolic());
-		assertEquals("refs/heads/master", h.getTarget().getName());
+		new File(db.getDirectory(), "refs/heads").mkdirs();
 
-		Ref b = db.exactRef("refs/heads/b");
-		assertFalse(b.isSymbolic());
-		assertTrue(b.isPeeled());
-		assertEquals(bCommit, b.getObjectId().name());
+		String invalidId = "deadbeefdeadbeefdeadbeefdeadbeefdeadbeef";
+		File headFile = new File(db.getDirectory(), "refs/heads/broken");
+		try (OutputStream os = new FileOutputStream(headFile)) {
+			os.write(Constants.encodeASCII(invalidId + "\n"));
+		}
 
-		assertFalse(db.getRefDatabase().hasFastTipsWithSha1());
+		Ref r = db.exactRef("refs/heads/broken");
+		assertNotNull(r);
+		db.convertToReftable(true, false);
 	}
 
 	@Test
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/reftable/ReftableTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/reftable/ReftableTest.java
index 0d739b9276..ea0d92acfd 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/reftable/ReftableTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/reftable/ReftableTest.java
@@ -941,6 +941,12 @@ public class ReftableTest {
 			}
 			assertFalse(lc.next());
 		}
+
+		for (Ref exp : refs) {
+ 			try (LogCursor lc = t.seekLog(exp.getName())) {
+				assertTrue("has " + exp.getName(), lc.next());
+			}
+		}
 	}
 
 	@Test
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/revwalk/RevWalkMergedIntoTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/revwalk/RevWalkMergedIntoTest.java
index 2f16aa49e8..2754bd36ae 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/revwalk/RevWalkMergedIntoTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/revwalk/RevWalkMergedIntoTest.java
@@ -99,7 +99,7 @@ public class RevWalkMergedIntoTest extends RevWalkTestCase {
 		createBranch(commit(commit(a)), b);
 		createBranch(commit(commit(i)), c);
 
-		assertTrue( rw.isMergedIntoAny(a, getRefs()));
+		assertTrue(rw.isMergedIntoAny(a, getRefs()));
 	}
 
 	@Test
@@ -125,4 +125,23 @@ public class RevWalkMergedIntoTest extends RevWalkTestCase {
 
 		assertTrue(rw.isMergedIntoAll(a, getRefs()));
 	}
+
+	@Test
+	public void testMergeIntoAnnotatedTag() throws Exception {
+		/*
+		 *        a
+		 *        |
+		 *        b
+		 *       / \
+		 *      c  v1 (annotated tag)
+		 */
+		String c = "refs/heads/c";
+		String v1 = "refs/tags/v1";
+		final RevCommit a = commit();
+		final RevCommit b = commit(a);
+		createBranch(commit(b), c);
+		createBranch(tag("v1", b), v1);
+
+		assertTrue(rw.isMergedIntoAll(a, getRefs()));
+	}
 }
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/revwalk/RevWalkUtilsReachableTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/revwalk/RevWalkUtilsReachableTest.java
index 200cb6a4fe..0a045c917b 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/revwalk/RevWalkUtilsReachableTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/revwalk/RevWalkUtilsReachableTest.java
@@ -82,20 +82,33 @@ public class RevWalkUtilsReachableTest extends RevWalkTestCase {
 		 *  a   b
 		 *  |   |
 		 *  c   d
+		 *      | \
+		 *      f  e
+		 *      | /
+		 *      g
 		 */
 		RevCommit a = commit();
 		RevCommit b = commit();
 		RevCommit c = commit(a);
 		RevCommit d = commit(b);
+		RevCommit f = commit(d);
+		RevCommit e = commit(d);
+		RevCommit g = commit(f, e);
 		Ref branchA = branch("a", a);
 		Ref branchB = branch("b", b);
 		Ref branchC = branch("c", c);
 		Ref branchD = branch("d", d);
+		Ref branchE = branch("e", e);
+		Ref branchF = branch("f", f);
+		Ref branchG = branch("g", g);
 
 		assertContains(a, asList(branchA, branchC));
-		assertContains(b, asList(branchB, branchD));
+		assertContains(b, asList(branchB, branchD, branchE, branchF, branchG));
 		assertContains(c, asList(branchC));
-		assertContains(d, asList(branchD));
+		assertContains(d, asList(branchD, branchE, branchF, branchG));
+		assertContains(e, asList(branchE, branchG));
+		assertContains(f, asList(branchF, branchG));
+		assertContains(g, asList(branchG));
 	}
 
 	private Ref branch(String name, RevCommit dst) throws Exception {
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/UploadPackLsRefsFileRepositoryTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/UploadPackLsRefsFileRepositoryTest.java
new file mode 100644
index 0000000000..7d5fc61017
--- /dev/null
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/UploadPackLsRefsFileRepositoryTest.java
@@ -0,0 +1,123 @@
+/*
+ * Copyright (C) 2021, Saša Živkov <sasa.zivkov@sap.com> 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
+ * https://www.eclipse.org/org/documents/edl-v10.php.
+ *
+ * SPDX-License-Identifier: BSD-3-Clause
+ */
+package org.eclipse.jgit.transport;
+
+import static org.hamcrest.MatcherAssert.assertThat;
+import static org.hamcrest.Matchers.is;
+import static org.junit.Assert.assertTrue;
+
+import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
+import java.io.IOException;
+import java.util.Objects;
+import java.util.function.Consumer;
+
+import org.eclipse.jgit.internal.storage.file.FileRepository;
+import org.eclipse.jgit.junit.LocalDiskRepositoryTestCase;
+import org.eclipse.jgit.junit.TestRepository;
+import org.eclipse.jgit.lib.Sets;
+import org.eclipse.jgit.revwalk.RevCommit;
+import org.eclipse.jgit.revwalk.RevTag;
+import org.junit.Before;
+import org.junit.Test;
+
+// TODO: refactor UploadPackTest to run against both DfsRepository and FileRepository
+public class UploadPackLsRefsFileRepositoryTest
+		extends LocalDiskRepositoryTestCase {
+
+	private FileRepository server;
+
+	private TestRepository<FileRepository> remote;
+
+	@Before
+	@Override
+	public void setUp() throws Exception {
+		super.setUp();
+		server = createWorkRepository();
+		remote = new TestRepository<>(server);
+	}
+
+	@Test
+	public void testV2LsRefsPeel() throws Exception {
+		RevCommit tip = remote.commit().message("message").create();
+		remote.update("master", tip);
+		server.updateRef("HEAD").link("refs/heads/master");
+		RevTag tag = remote.tag("tag", tip);
+		remote.update("refs/tags/tag", tag);
+
+		ByteArrayInputStream recvStream = uploadPackV2("command=ls-refs\n",
+				PacketLineIn.delimiter(), "peel", PacketLineIn.end());
+		PacketLineIn pckIn = new PacketLineIn(recvStream);
+
+		assertThat(pckIn.readString(),
+				is(tip.toObjectId().getName() + " HEAD"));
+		assertThat(pckIn.readString(),
+				is(tip.toObjectId().getName() + " refs/heads/master"));
+		assertThat(pckIn.readString(), is(tag.toObjectId().getName()
+				+ " refs/tags/tag peeled:" + tip.toObjectId().getName()));
+		assertTrue(PacketLineIn.isEnd(pckIn.readString()));
+	}
+
+	private ByteArrayInputStream uploadPackV2(String... inputLines)
+			throws Exception {
+		return uploadPackV2(null, inputLines);
+	}
+
+	private ByteArrayInputStream uploadPackV2(
+			Consumer<UploadPack> postConstructionSetup, String... inputLines)
+			throws Exception {
+		ByteArrayInputStream recvStream = uploadPackV2Setup(
+				postConstructionSetup, inputLines);
+		PacketLineIn pckIn = new PacketLineIn(recvStream);
+
+		// drain capabilities
+		while (!PacketLineIn.isEnd(pckIn.readString())) {
+			// do nothing
+		}
+		return recvStream;
+	}
+
+	private ByteArrayInputStream uploadPackV2Setup(
+			Consumer<UploadPack> postConstructionSetup, String... inputLines)
+			throws Exception {
+
+		ByteArrayInputStream send = linesAsInputStream(inputLines);
+
+		server.getConfig().setString("protocol", null, "version", "2");
+		UploadPack up = new UploadPack(server);
+		if (postConstructionSetup != null) {
+			postConstructionSetup.accept(up);
+		}
+		up.setExtraParameters(Sets.of("version=2"));
+
+		ByteArrayOutputStream recv = new ByteArrayOutputStream();
+		up.upload(send, recv, null);
+
+		return new ByteArrayInputStream(recv.toByteArray());
+	}
+
+	private static ByteArrayInputStream linesAsInputStream(String... inputLines)
+			throws IOException {
+		try (ByteArrayOutputStream send = new ByteArrayOutputStream()) {
+			PacketLineOut pckOut = new PacketLineOut(send);
+			for (String line : inputLines) {
+				Objects.requireNonNull(line);
+				if (PacketLineIn.isEnd(line)) {
+					pckOut.end();
+				} else if (PacketLineIn.isDelimiter(line)) {
+					pckOut.writeDelim();
+				} else {
+					pckOut.writeString(line);
+				}
+			}
+			return new ByteArrayInputStream(send.toByteArray());
+		}
+	}
+}