Add worktrees read support

Based on deritative work done in Andre's work in [1].

This change focuses on adding support for reading the repository
state when branches are checked out using git's worktrees.

I've refactored original work by removing all unrelevant
changes which were mostly around refactoring to extract
i.e. constants which mostly created noise for a review.

I've tried to address original review comments:
- Not adding non-behavioral changes
- "HEAD" should get resolved from gitDir
- Reftable recently landed in cgit 2.45,
  see https://github.com/git/git/blob/master/Documentation/RelNotes/2.45.0.txt#L8
  We can add worktree support for reftable in a later change.
- Some new tests to read from a linked worktree which
  is created manually as there's no write support.

[1] https://git.eclipse.org/r/c/jgit/jgit/+/163940/18

Change-Id: Id077d58fb6c09ecb090eb09d5dbc7edc351a581d

9 files changed, 215 insertions, 22 deletions

diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/EolRepositoryTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/EolRepositoryTest.java
index b937b1f6a9..4c971ffb6b 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/EolRepositoryTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/EolRepositoryTest.java
@@ -559,7 +559,7 @@ public class EolRepositoryTest extends RepositoryTestCase {
 
 		}
 		if (infoAttributesContent != null) {
-			File f = new File(db.getDirectory(), Constants.INFO_ATTRIBUTES);
+			File f = new File(db.getCommonDirectory(), Constants.INFO_ATTRIBUTES);
 			write(f, infoAttributesContent);
 		}
 		config.save();
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/LinkedWorktreeTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/LinkedWorktreeTest.java
new file mode 100644
index 0000000000..3b60e1b5c0
--- /dev/null
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/LinkedWorktreeTest.java
@@ -0,0 +1,192 @@
+/*
+ * Copyright (C) 2024, Broadcom 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.api;
+
+import static org.eclipse.jgit.lib.Constants.HEAD;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+
+import java.io.ByteArrayInputStream;
+import java.io.File;
+import java.io.IOException;
+import java.nio.charset.StandardCharsets;
+import java.util.Collection;
+import java.util.Iterator;
+
+import org.eclipse.jgit.internal.storage.file.FileRepository;
+import org.eclipse.jgit.junit.JGitTestUtil;
+import org.eclipse.jgit.junit.RepositoryTestCase;
+import org.eclipse.jgit.lib.ObjectId;
+import org.eclipse.jgit.lib.ReflogEntry;
+import org.eclipse.jgit.revwalk.RevCommit;
+import org.eclipse.jgit.util.FS;
+import org.eclipse.jgit.util.FS.ExecutionResult;
+import org.eclipse.jgit.util.RawParseUtils;
+import org.eclipse.jgit.util.TemporaryBuffer;
+import org.junit.Test;
+
+public class LinkedWorktreeTest extends RepositoryTestCase {
+
+	@Override
+	public void setUp() throws Exception {
+		super.setUp();
+
+		try (Git git = new Git(db)) {
+			git.commit().setMessage("Initial commit").call();
+		}
+	}
+
+	@Test
+	public void testWeCanReadFromLinkedWorktreeFromBare() throws Exception {
+		FS fs = db.getFS();
+		File directory = trash.getParentFile();
+		String dbDirName = db.getWorkTree().getName();
+		cloneBare(fs, directory, dbDirName, "bare");
+		File bareDirectory = new File(directory, "bare");
+		worktreeAddExisting(fs, bareDirectory, "master");
+
+		File worktreesDir = new File(bareDirectory, "worktrees");
+		File masterWorktreesDir = new File(worktreesDir, "master");
+
+		FileRepository repository = new FileRepository(masterWorktreesDir);
+		try (Git git = new Git(repository)) {
+			ObjectId objectId = repository.resolve(HEAD);
+			assertNotNull(objectId);
+
+			Iterator<RevCommit> log = git.log().all().call().iterator();
+			assertTrue(log.hasNext());
+			assertTrue("Initial commit".equals(log.next().getShortMessage()));
+
+			// we have reflog entry
+			// depending on git version we either have one or
+			// two entries where extra is zeroid entry with
+			// same message or no message
+			Collection<ReflogEntry> reflog = git.reflog().call();
+			assertNotNull(reflog);
+			assertTrue(reflog.size() > 0);
+			ReflogEntry[] reflogs = reflog.toArray(new ReflogEntry[0]);
+			assertEquals(reflogs[reflogs.length - 1].getComment(),
+					"reset: moving to HEAD");
+
+			// index works with file changes
+			File masterDir = new File(directory, "master");
+			File testFile = new File(masterDir, "test");
+
+			Status status = git.status().call();
+			assertTrue(status.getUncommittedChanges().size() == 0);
+			assertTrue(status.getUntracked().size() == 0);
+
+			JGitTestUtil.write(testFile, "test");
+			status = git.status().call();
+			assertTrue(status.getUncommittedChanges().size() == 0);
+			assertTrue(status.getUntracked().size() == 1);
+
+			git.add().addFilepattern("test").call();
+			status = git.status().call();
+			assertTrue(status.getUncommittedChanges().size() == 1);
+			assertTrue(status.getUntracked().size() == 0);
+		}
+	}
+
+	@Test
+	public void testWeCanReadFromLinkedWorktreeFromNonBare() throws Exception {
+		FS fs = db.getFS();
+		worktreeAddNew(fs, db.getWorkTree(), "wt");
+
+		File worktreesDir = new File(db.getDirectory(), "worktrees");
+		File masterWorktreesDir = new File(worktreesDir, "wt");
+
+		FileRepository repository = new FileRepository(masterWorktreesDir);
+		try (Git git = new Git(repository)) {
+			ObjectId objectId = repository.resolve(HEAD);
+			assertNotNull(objectId);
+
+			Iterator<RevCommit> log = git.log().all().call().iterator();
+			assertTrue(log.hasNext());
+			assertTrue("Initial commit".equals(log.next().getShortMessage()));
+
+			// we have reflog entry
+			Collection<ReflogEntry> reflog = git.reflog().call();
+			assertNotNull(reflog);
+			assertTrue(reflog.size() > 0);
+			ReflogEntry[] reflogs = reflog.toArray(new ReflogEntry[0]);
+			assertEquals(reflogs[reflogs.length - 1].getComment(),
+					"reset: moving to HEAD");
+
+			// index works with file changes
+			File directory = trash.getParentFile();
+			File wtDir = new File(directory, "wt");
+			File testFile = new File(wtDir, "test");
+
+			Status status = git.status().call();
+			assertTrue(status.getUncommittedChanges().size() == 0);
+			assertTrue(status.getUntracked().size() == 0);
+
+			JGitTestUtil.write(testFile, "test");
+			status = git.status().call();
+			assertTrue(status.getUncommittedChanges().size() == 0);
+			assertTrue(status.getUntracked().size() == 1);
+
+			git.add().addFilepattern("test").call();
+			status = git.status().call();
+			assertTrue(status.getUncommittedChanges().size() == 1);
+			assertTrue(status.getUntracked().size() == 0);
+		}
+
+	}
+
+	private static void cloneBare(FS fs, File directory, String from, String to) throws IOException, InterruptedException {
+		ProcessBuilder builder = fs.runInShell("git",
+				new String[] { "clone", "--bare", from, to });
+		builder.directory(directory);
+		builder.environment().put("HOME", fs.userHome().getAbsolutePath());
+		StringBuilder input = new StringBuilder();
+		ExecutionResult result = fs.execute(builder, new ByteArrayInputStream(
+				input.toString().getBytes(StandardCharsets.UTF_8)));
+		String stdOut = toString(result.getStdout());
+		String errorOut = toString(result.getStderr());
+		assertNotNull(stdOut);
+		assertNotNull(errorOut);
+	}
+
+	private static void worktreeAddExisting(FS fs, File directory, String name) throws IOException, InterruptedException {
+		ProcessBuilder builder = fs.runInShell("git",
+				new String[] { "worktree", "add", "../" + name, name });
+		builder.directory(directory);
+		builder.environment().put("HOME", fs.userHome().getAbsolutePath());
+		StringBuilder input = new StringBuilder();
+		ExecutionResult result = fs.execute(builder, new ByteArrayInputStream(
+				input.toString().getBytes(StandardCharsets.UTF_8)));
+		String stdOut = toString(result.getStdout());
+		String errorOut = toString(result.getStderr());
+		assertNotNull(stdOut);
+		assertNotNull(errorOut);
+	}
+
+	private static void worktreeAddNew(FS fs, File directory, String name) throws IOException, InterruptedException {
+		ProcessBuilder builder = fs.runInShell("git",
+				new String[] { "worktree", "add", "-b", name, "../" + name, "master"});
+		builder.directory(directory);
+		builder.environment().put("HOME", fs.userHome().getAbsolutePath());
+		StringBuilder input = new StringBuilder();
+		ExecutionResult result = fs.execute(builder, new ByteArrayInputStream(
+				input.toString().getBytes(StandardCharsets.UTF_8)));
+		String stdOut = toString(result.getStdout());
+		String errorOut = toString(result.getStderr());
+		assertNotNull(stdOut);
+		assertNotNull(errorOut);
+	}
+
+	private static String toString(TemporaryBuffer b) throws IOException {
+		return RawParseUtils.decode(b.toByteArray());
+	}
+
+}
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/attributes/AttributesHandlerTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/attributes/AttributesHandlerTest.java
index 7fb98ec53b..c41dd81add 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/attributes/AttributesHandlerTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/attributes/AttributesHandlerTest.java
@@ -584,7 +584,7 @@ public class AttributesHandlerTest extends RepositoryTestCase {
 
 		}
 		if (infoAttributesContent != null) {
-			File f = new File(db.getDirectory(), Constants.INFO_ATTRIBUTES);
+			File f = new File(db.getCommonDirectory(), Constants.INFO_ATTRIBUTES);
 			write(f, infoAttributesContent);
 		}
 		config.save();
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/BatchRefUpdateTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/BatchRefUpdateTest.java
index daf4382719..1af42cb229 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/BatchRefUpdateTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/BatchRefUpdateTest.java
@@ -171,7 +171,7 @@ public class BatchRefUpdateTest extends LocalDiskRepositoryTestCase {
 			assertEquals(c2.getResult(), ReceiveCommand.Result.OK);
 		}
 
-		File packed = new File(diskRepo.getDirectory(), "packed-refs");
+		File packed = new File(diskRepo.getCommonDirectory(), "packed-refs");
 		String packedStr = new String(Files.readAllBytes(packed.toPath()),
 				UTF_8);
 
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/GcPackRefsTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/GcPackRefsTest.java
index 8baa3cc341..c57295518d 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/GcPackRefsTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/GcPackRefsTest.java
@@ -58,7 +58,7 @@ public class GcPackRefsTest extends GcTestCase {
 		String ref = "dir/ref";
 		tr.branch(ref).commit().create();
 		String name = repo.findRef(ref).getName();
-		Path dir = repo.getDirectory().toPath().resolve(name).getParent();
+		Path dir = repo.getCommonDirectory().toPath().resolve(name).getParent();
 		assertNotNull(dir);
 		gc.packRefs();
 		assertFalse(Files.exists(dir));
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/GcReflogTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/GcReflogTest.java
index e6c1ee5fd6..29f180d76b 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/GcReflogTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/GcReflogTest.java
@@ -30,7 +30,7 @@ public class GcReflogTest extends GcTestCase {
 		BranchBuilder bb = tr.branch("refs/heads/master");
 		bb.commit().add("A", "A").add("B", "B").create();
 		bb.commit().add("A", "A2").add("B", "B2").create();
-		new File(repo.getDirectory(), Constants.LOGS + "/refs/heads/master")
+		new File(repo.getCommonDirectory(), Constants.LOGS + "/refs/heads/master")
 				.delete();
 		stats = gc.getStatistics();
 		assertEquals(8, stats.numberOfLooseObjects);
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/RefDirectoryTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/RefDirectoryTest.java
index 2bafde65d3..baa0182b87 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/RefDirectoryTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/RefDirectoryTest.java
@@ -90,25 +90,26 @@ public class RefDirectoryTest extends LocalDiskRepositoryTestCase {
 	@Test
 	public void testCreate() throws IOException {
 		// setUp above created the directory. We just have to test it.
-		File d = diskRepo.getDirectory();
+		File gitDir = diskRepo.getDirectory();
+		File commonDir = diskRepo.getCommonDirectory();
 		assertSame(diskRepo, refdir.getRepository());
 
-		assertTrue(new File(d, "refs").isDirectory());
-		assertTrue(new File(d, "logs").isDirectory());
-		assertTrue(new File(d, "logs/refs").isDirectory());
-		assertFalse(new File(d, "packed-refs").exists());
+		assertTrue(new File(commonDir, "refs").isDirectory());
+		assertTrue(new File(commonDir, "logs").isDirectory());
+		assertTrue(new File(commonDir, "logs/refs").isDirectory());
+		assertFalse(new File(commonDir, "packed-refs").exists());
 
-		assertTrue(new File(d, "refs/heads").isDirectory());
-		assertTrue(new File(d, "refs/tags").isDirectory());
-		assertEquals(2, new File(d, "refs").list().length);
-		assertEquals(0, new File(d, "refs/heads").list().length);
-		assertEquals(0, new File(d, "refs/tags").list().length);
+		assertTrue(new File(commonDir, "refs/heads").isDirectory());
+		assertTrue(new File(commonDir, "refs/tags").isDirectory());
+		assertEquals(2, new File(commonDir, "refs").list().length);
+		assertEquals(0, new File(commonDir, "refs/heads").list().length);
+		assertEquals(0, new File(commonDir, "refs/tags").list().length);
 
-		assertTrue(new File(d, "logs/refs/heads").isDirectory());
-		assertFalse(new File(d, "logs/HEAD").exists());
-		assertEquals(0, new File(d, "logs/refs/heads").list().length);
+		assertTrue(new File(commonDir, "logs/refs/heads").isDirectory());
+		assertFalse(new File(gitDir, "logs/HEAD").exists());
+		assertEquals(0, new File(commonDir, "logs/refs/heads").list().length);
 
-		assertEquals("ref: refs/heads/master\n", read(new File(d, HEAD)));
+		assertEquals("ref: refs/heads/master\n", read(new File(gitDir, HEAD)));
 	}
 
 	@Test(expected = UnsupportedOperationException.class)
@@ -1382,7 +1383,7 @@ public class RefDirectoryTest extends LocalDiskRepositoryTestCase {
 	}
 
 	private void deleteLooseRef(String name) {
-		File path = new File(diskRepo.getDirectory(), name);
+		File path = new File(diskRepo.getCommonDirectory(), name);
 		assertTrue("deleted " + name, path.delete());
 	}
 }
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/ReflogReaderTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/ReflogReaderTest.java
index dc0e749373..eb521ff9eb 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/ReflogReaderTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/ReflogReaderTest.java
@@ -238,7 +238,7 @@ public class ReflogReaderTest extends SampleDataRepositoryTestCase {
 
 	private void setupReflog(String logName, byte[] data)
 			throws FileNotFoundException, IOException {
-		File logfile = new File(db.getDirectory(), logName);
+		File logfile = new File(db.getCommonDirectory(), logName);
 		if (!logfile.getParentFile().mkdirs()
 				&& !logfile.getParentFile().isDirectory()) {
 			throw new IOException(
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/ReflogWriterTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/ReflogWriterTest.java
index 8d0e99dea0..8e9b7b84bd 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/ReflogWriterTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/ReflogWriterTest.java
@@ -48,7 +48,7 @@ public class ReflogWriterTest extends SampleDataRepositoryTestCase {
 
 	private void readReflog(byte[] buffer)
 			throws FileNotFoundException, IOException {
-		File logfile = new File(db.getDirectory(), "logs/refs/heads/master");
+		File logfile = new File(db.getCommonDirectory(), "logs/refs/heads/master");
 		if (!logfile.getParentFile().mkdirs()
 				&& !logfile.getParentFile().isDirectory()) {
 			throw new IOException(