Merge branch 'master' into stable-6.2

* master:
  RewriteGenerator: Fully buffering of input is no longer necessary
  Update Orbit to S20220517184036
  PackFileSnapshot: Resolve warnings by using "equals" instead of "=="
  Remove stray files (probes or lock files) created by background threads

Change-Id: I1522fcd03fb7ef0d7512b5d0b3bc09271e918c48

8 files changed, 134 insertions, 32 deletions

diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackFileSnapshot.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackFileSnapshot.java
index 17bd863528..a784af8c3f 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackFileSnapshot.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackFileSnapshot.java
@@ -15,6 +15,7 @@ import java.io.RandomAccessFile;
 
 import org.eclipse.jgit.lib.AnyObjectId;
 import org.eclipse.jgit.lib.ObjectId;
+import org.eclipse.jgit.util.Equality;
 
 class PackFileSnapshot extends FileSnapshot {
 
@@ -61,7 +62,8 @@ class PackFileSnapshot extends FileSnapshot {
 	}
 
 	boolean isChecksumChanged(File packFile) {
-		return wasChecksumChanged = checksum != MISSING_CHECKSUM
+		return wasChecksumChanged = !Equality.isSameInstance(checksum,
+				MISSING_CHECKSUM)
 				&& !checksum.equals(readChecksum(packFile));
 	}
 
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/revwalk/RevWalk.java b/org.eclipse.jgit/src/org/eclipse/jgit/revwalk/RevWalk.java
index a50eaf1a8a..a25948e50b 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/revwalk/RevWalk.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/revwalk/RevWalk.java
@@ -143,8 +143,19 @@ public class RevWalk implements Iterable<RevCommit>, AutoCloseable {
 	 */
 	static final int TOPO_QUEUED = 1 << 6;
 
+	/**
+	 * Set on a RevCommit when a {@link TreeRevFilter} has been applied.
+	 * <p>
+	 * This flag is processed by the {@link RewriteGenerator} to check if a
+	 * {@link TreeRevFilter} has been applied.
+	 *
+	 * @see TreeRevFilter
+	 * @see RewriteGenerator
+	 */
+	static final int TREE_REV_FILTER_APPLIED = 1 << 7;
+
 	/** Number of flag bits we keep internal for our own use. See above flags. */
-	static final int RESERVED_FLAGS = 7;
+	static final int RESERVED_FLAGS = 8;
 
 	private static final int APP_FLAGS = -1 & ~((1 << RESERVED_FLAGS) - 1);
 
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/revwalk/RewriteGenerator.java b/org.eclipse.jgit/src/org/eclipse/jgit/revwalk/RewriteGenerator.java
index 4565a4b5de..1adef07ad9 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/revwalk/RewriteGenerator.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/revwalk/RewriteGenerator.java
@@ -24,14 +24,7 @@ import org.eclipse.jgit.errors.MissingObjectException;
  * commit that matched the revision walker's filters.
  * <p>
  * This generator is the second phase of a path limited revision walk and
- * assumes it is receiving RevCommits from {@link TreeRevFilter},
- * after they have been fully buffered by {@link AbstractRevQueue}. The full
- * buffering is necessary to allow the simple loop used within our own
- * {@link #rewrite(RevCommit)} to pull completely through a strand of
- * {@link RevWalk#REWRITE} colored commits and come up with a simplification
- * that makes the DAG dense. Not fully buffering the commits first would cause
- * this loop to abort early, due to commits not being parsed and colored
- * correctly.
+ * assumes it is receiving RevCommits from {@link TreeRevFilter}.
  *
  * @see TreeRevFilter
  */
@@ -43,9 +36,12 @@ class RewriteGenerator extends Generator {
 
 	private final Generator source;
 
+	private final FIFORevQueue pending;
+
 	RewriteGenerator(Generator s) {
 		super(s.firstParent);
 		source = s;
+		pending = new FIFORevQueue(s.firstParent);
 	}
 
 	@Override
@@ -62,10 +58,19 @@ class RewriteGenerator extends Generator {
 	@Override
 	RevCommit next() throws MissingObjectException,
 			IncorrectObjectTypeException, IOException {
-		final RevCommit c = source.next();
+		RevCommit c = pending.next();
+
 		if (c == null) {
-			return null;
+			c = source.next();
+			if (c == null) {
+				// We are done: Both the source generator and our internal list
+				// are completely exhausted.
+				return null;
+			}
 		}
+
+		applyFilterToParents(c);
+
 		boolean rewrote = false;
 		final RevCommit[] pList = c.parents;
 		final int nParents = pList.length;
@@ -91,10 +96,41 @@ class RewriteGenerator extends Generator {
 		return c;
 	}
 
-	private RevCommit rewrite(RevCommit p) {
+	/**
+	 * Makes sure that the {@link TreeRevFilter} has been applied to all parents
+	 * of this commit by the previous {@link PendingGenerator}.
+	 *
+	 * @param c
+	 * @throws MissingObjectException
+	 * @throws IncorrectObjectTypeException
+	 * @throws IOException
+	 */
+	private void applyFilterToParents(RevCommit c)
+			throws MissingObjectException, IncorrectObjectTypeException,
+			IOException {
+		for (RevCommit parent : c.parents) {
+			while ((parent.flags & RevWalk.TREE_REV_FILTER_APPLIED) == 0) {
+
+				RevCommit n = source.next();
+
+				if (n != null) {
+					pending.add(n);
+				} else {
+					// Source generator is exhausted; filter has been applied to
+					// all commits
+					return;
+				}
+
+			}
+
+		}
+	}
+
+	private RevCommit rewrite(RevCommit p) throws MissingObjectException,
+			IncorrectObjectTypeException, IOException {
 		for (;;) {
-			final RevCommit[] pList = p.parents;
-			if (pList.length > 1) {
+
+			if (p.parents.length > 1) {
 				// This parent is a merge, so keep it.
 				//
 				return p;
@@ -114,14 +150,16 @@ class RewriteGenerator extends Generator {
 				return p;
 			}
 
-			if (pList.length == 0) {
+			if (p.parents.length == 0) {
 				// We can't go back any further, other than to
 				// just delete the parent entirely.
 				//
 				return null;
 			}
 
-			p = pList[0];
+			applyFilterToParents(p.parents[0]);
+			p = p.parents[0];
+
 		}
 	}
 
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/revwalk/StartGenerator.java b/org.eclipse.jgit/src/org/eclipse/jgit/revwalk/StartGenerator.java
index bfcea6ea8f..a79901ca10 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/revwalk/StartGenerator.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/revwalk/StartGenerator.java
@@ -125,12 +125,6 @@ class StartGenerator extends Generator {
 		}
 
 		if ((g.outputType() & NEEDS_REWRITE) != 0) {
-			// Correction for an upstream NEEDS_REWRITE is to buffer
-			// fully and then apply a rewrite generator that can
-			// pull through the rewrite chain and produce a dense
-			// output graph.
-			//
-			g = new FIFORevQueue(g);
 			g = new RewriteGenerator(g);
 		}
 
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/revwalk/TreeRevFilter.java b/org.eclipse.jgit/src/org/eclipse/jgit/revwalk/TreeRevFilter.java
index 822fc5320c..92d72268d1 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/revwalk/TreeRevFilter.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/revwalk/TreeRevFilter.java
@@ -41,6 +41,8 @@ public class TreeRevFilter extends RevFilter {
 
 	private static final int UNINTERESTING = RevWalk.UNINTERESTING;
 
+	private static final int FILTER_APPLIED = RevWalk.TREE_REV_FILTER_APPLIED;
+
 	private final int rewriteFlag;
 	private final TreeWalk pathFilter;
 
@@ -101,6 +103,7 @@ public class TreeRevFilter extends RevFilter {
 	public boolean include(RevWalk walker, RevCommit c)
 			throws StopWalkException, MissingObjectException,
 			IncorrectObjectTypeException, IOException {
+		c.flags |= FILTER_APPLIED;
 		// Reset the tree filter to scan this commit and parents.
 		//
 		RevCommit[] pList = c.parents;
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/storage/file/FileBasedConfig.java b/org.eclipse.jgit/src/org/eclipse/jgit/storage/file/FileBasedConfig.java
index 567e40936a..cba5e1697c 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/storage/file/FileBasedConfig.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/storage/file/FileBasedConfig.java
@@ -180,9 +180,10 @@ public class FileBasedConfig extends StoredConfig {
 		}
 
 		final LockFile lf = new LockFile(getFile());
-		if (!lf.lock())
-			throw new LockFailedException(getFile());
 		try {
+			if (!lf.lock()) {
+				throw new LockFailedException(getFile());
+			}
 			lf.setNeedSnapshotNoConfig(true);
 			lf.write(out);
 			if (!lf.commit())
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/util/Equality.java b/org.eclipse.jgit/src/org/eclipse/jgit/util/Equality.java
new file mode 100644
index 0000000000..da1684630b
--- /dev/null
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/util/Equality.java
@@ -0,0 +1,36 @@
+/*
+ * Copyright (C) 2022, Fabio Ponciroli <ponch78@gmail.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.util;
+
+/**
+ * Equality utilities.
+ *
+ * @since: 6.2
+ */
+public class Equality {
+
+    /**
+     * Compare by reference
+     *
+     * @param a
+     *            First object to compare
+     * @param b
+     *            Second object to compare
+     * @return {@code true} if the objects are identical, {@code false}
+     *         otherwise
+     *
+     * @since 6.2
+     */
+    @SuppressWarnings("ReferenceEquality")
+    public static <T> boolean isSameInstance(T a, T b) {
+        return a == b;
+    }
+}
\ No newline at end of file
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/util/FS.java b/org.eclipse.jgit/src/org/eclipse/jgit/util/FS.java
index 9237c0a9b2..e8f38d8fd9 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/util/FS.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/util/FS.java
@@ -47,7 +47,6 @@ import java.util.concurrent.CancellationException;
 import java.util.concurrent.CompletableFuture;
 import java.util.concurrent.ConcurrentHashMap;
 import java.util.concurrent.ExecutionException;
-import java.util.concurrent.Executor;
 import java.util.concurrent.ExecutorService;
 import java.util.concurrent.Executors;
 import java.util.concurrent.LinkedBlockingQueue;
@@ -262,8 +261,9 @@ public abstract class FS {
 		 *
 		 * @see java.util.concurrent.Executors#newCachedThreadPool()
 		 */
-		private static final Executor FUTURE_RUNNER = new ThreadPoolExecutor(0,
-				5, 30L, TimeUnit.SECONDS, new LinkedBlockingQueue<Runnable>(),
+		private static final ExecutorService FUTURE_RUNNER = new ThreadPoolExecutor(
+				0, 5, 30L, TimeUnit.SECONDS,
+				new LinkedBlockingQueue<Runnable>(),
 				runnable -> {
 					Thread t = new Thread(runnable,
 							"JGit-FileStoreAttributeReader-" //$NON-NLS-1$
@@ -285,8 +285,9 @@ public abstract class FS {
 		 * small keep-alive time to avoid delays on shut-down.
 		 * </p>
 		 */
-		private static final Executor SAVE_RUNNER = new ThreadPoolExecutor(0, 1,
-				1L, TimeUnit.MILLISECONDS, new LinkedBlockingQueue<Runnable>(),
+		private static final ExecutorService SAVE_RUNNER = new ThreadPoolExecutor(
+				0, 1, 1L, TimeUnit.MILLISECONDS,
+				new LinkedBlockingQueue<Runnable>(),
 				runnable -> {
 					Thread t = new Thread(runnable,
 							"JGit-FileStoreAttributeWriter-" //$NON-NLS-1$
@@ -296,6 +297,18 @@ public abstract class FS {
 					return t;
 				});
 
+		static {
+			// Shut down the SAVE_RUNNER on System.exit()
+			Runtime.getRuntime().addShutdownHook(new Thread(() -> {
+				try {
+					SAVE_RUNNER.shutdownNow();
+					SAVE_RUNNER.awaitTermination(100, TimeUnit.MILLISECONDS);
+				} catch (Exception e) {
+					// Ignore; we're shutting down
+				}
+			}));
+		}
+
 		/**
 		 * Whether FileStore attributes should be determined asynchronously
 		 *
@@ -452,11 +465,13 @@ public abstract class FS {
 					return null;
 				}
 				// fall through and return fallback
-			} catch (IOException | InterruptedException
-					| ExecutionException | CancellationException e) {
+			} catch (IOException | ExecutionException | CancellationException e) {
 				LOG.error(e.getMessage(), e);
 			} catch (TimeoutException | SecurityException e) {
 				// use fallback
+			} catch (InterruptedException e) {
+				LOG.error(e.getMessage(), e);
+				Thread.currentThread().interrupt();
 			}
 			LOG.debug("{}: use fallback timestamp resolution for directory {}", //$NON-NLS-1$
 					Thread.currentThread(), dir);
@@ -474,6 +489,7 @@ public abstract class FS {
 			Path probe = dir.resolve(".probe-" + UUID.randomUUID()); //$NON-NLS-1$
 			Instant end = Instant.now().plusSeconds(3);
 			try {
+				probe.toFile().deleteOnExit();
 				Files.createFile(probe);
 				do {
 					n++;
@@ -540,6 +556,7 @@ public abstract class FS {
 			}
 			Path probe = dir.resolve(".probe-" + UUID.randomUUID()); //$NON-NLS-1$
 			try {
+				probe.toFile().deleteOnExit();
 				Files.createFile(probe);
 				Duration fsResolution = getFsResolution(s, dir, probe);
 				Duration clockResolution = measureClockResolution();