Merge branch 'stable-5.4'

* stable-5.4: (82 commits)
  Export all packages of o.e.j.ant and o.e.j.archive bundles
  Do not require test bundles to export all packages
  Fix API problem filters
  Increase severity of AmbiguousMethodReference to ERROR
  [error prone] suppress AmbiguousMethodReference in AnyLongObjectId
  [error prone] fix ReferenceEquality warning in CommitBuilder
  [error prone] suppress NonAtomicVolatileUpdate warning in SimpleLruCache
  [error prone] fix ReferenceEquality warning in CommitGraphPane#authorFor
  [error prone] fix ReferenceEquality warning in RevWalk#isMergedInto
  [error prone] fix ReferenceEquality warning in RefUpdate#updateImpl
  [error prone] fix ReferenceEquality warning in static equals methods
  [error prone] suppress AmbiguousMethodReference in AnyObjectId
  [error prone] fix "FutureReturnValueIgnored" error in FS
  Fix formatting and add missing braces in Repository#stripWorkDir
  Repository: fix reference comparison of Files
  MergeAlgorithm: Suppress Error Prone warning about reference equality
  Fix NarrowingCompoundAssignment warnings from Error Prone
  FS_POSIX: handle Files.getFileStore() failures
  Fix OpenSshConfigTest#config
  FileSnapshot: fix bug with timestamp thresholding
  In LockFile#waitForStatChange wait in units of file time resolution
  Cache FileStoreAttributeCache per directory
  Fix FileSnapshot#save(long) and FileSnapshot#save(Instant)
  Persist minimal racy threshold and allow manual configuration
  Measure minimum racy interval to auto-configure FileSnapshot
  Reuse FileUtils to recursively delete files created by tests
  Fix FileAttributeCache.toString()
  Add test for racy git detection in FileSnapshot
  Repeat RefDirectoryTest.testGetRef_DiscoversModifiedLoose 100 times
  Fix org.eclipse.jdt.core.prefs of org.eclipse.jgit.junit
  Add missing javadoc in org.eclipse.jgit.junit
  Enhance RepeatRule to report number of failures at the end
  Fix FileSnapshotTests for filesystem with high timestamp resolution
  Retry deleting test files in FileBasedConfigTest
  Measure filesystem timestamp resolution already in test setup
  Refactor FileSnapshotTest to use NIO APIs
  Measure stored timestamp resolution instead of time to touch file
  Handle CancellationException in FileStoreAttributeCache
  Fix FileSnapshot#saveNoConfig
  Use Instant for smudge time in DirCache and DirCacheEntry
  Use Instant instead of milliseconds for filesystem timestamp handling
  Workaround SecurityException in FS#getFsTimestampResolution
  Fix NPE in FS$FileStoreAttributeCache.getFsTimestampResolution
  FS: ignore AccessDeniedException when measuring timestamp resolution
  Add debug trace for FileSnapshot
  Use FileChannel.open to touch file and set mtime to now
  Persist filesystem timestamp resolution and allow manual configuration
  Increase bazel timeout for long running tests
  Bazel: Fix lint warning flagged by buildifier
  Update bazlets to latest version
  Bazel: Add missing dependencies for ArchiveCommandTest
  Bazel: Remove FileTreeIteratorWithTimeControl from BUILD file
  Add support for nanoseconds and microseconds for Config#getTimeUnit
  Optionally measure filesystem timestamp resolution asynchronously
  Delete unused FileTreeIteratorWithTimeControl
  FileSnapshot#equals: consider UNKNOWN_SIZE
  Timeout measuring file timestamp resolution after 2 seconds
  Fix RacyGitTests#testRacyGitDetection
  GlobalBundleCache: Fix ClassNewInstance warning from Error Prone
  IncorrectObjectTypeException: Fix typos in constructors' Javadoc
  Change RacyGitTests to create a racy git situation in a stable way
  Deprecate Constants.CHARACTER_ENCODING in favor of StandardCharsets.UTF_8
  Fix non-deterministic hash of archives created by ArchiveCommand
  Update Maven plugins ecj, plexus, error-prone
  Update Maven plugins and cleanup Maven warnings
  Make inner classes static where possible
  Error Prone: Increase severity of NonOverridingEquals to ERROR
  Error Prone: Increase severity of ImmutableEnumChecker to ERROR
  GitDateParser#ParseableSimpleDateFormat: Make formatStr private final
  BatchRefUpdateTest: Suppress ImmutableEnumChecker warning
  PacketLineIn: Suppress comparison warnings for END and DELIM
  FileSnapshot#toString: Suppress ReferenceEquality warnings
  Blame: Suppress ReferenceEquality warning for RevCommit instances
  Fix API problem filters
  pgm: add missing optional dependency to org.tukaani:xz
  NetscapeCookieFile: Make hash static and group overloaded write
  NetscapeCookieFile: Javadoc fixes
  Config: Handle reference-equality warning (and empty javadoc)
  Error Prone: Increase severity of ShortCircuitBoolean to ERROR
  ObjectWalk: Prefer boolean operators over logical operators in comparisons
  BasePackFetchConnection: Prefer boolean operators over logical operators in comparisons
  PackWriter: Prefer boolean operators over logical operators in comparisons

Change-Id: I825fd55bcb5345fb7afe066bf54ca50325f40acb
Signed-off-by: David Pursehouse <david.pursehouse@gmail.com>
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>

lib/BUILD

@@ -12,6 +12,7 @@ java_library(
     visibility = [
         "//org.eclipse.jgit.archive:__pkg__",
         "//org.eclipse.jgit.pgm.test:__pkg__",
+        "//org.eclipse.jgit.test:__pkg__",
     ],
     exports = ["@commons-compress//jar"],
 )

org.eclipse.jgit.ant.test/src/org/eclipse/jgit/ant/tasks/GitCloneTaskTest.java

@@ -65,12 +65,13 @@ public class GitCloneTaskTest extends LocalDiskRepositoryTestCase {
 
 	@Before
 	public void before() throws IOException {
+		dest = createTempFile();
+		FS.getFileStoreAttributes(dest.toPath().getParent());
 		project = new Project();
 		project.init();
 		enableLogging();
 		project.addTaskDefinition("git-clone", GitCloneTask.class);
 		task = (GitCloneTask) project.createTask("git-clone");
-		dest = createTempFile();
 		task.setDest(dest);
 	}
 

org.eclipse.jgit.ant/META-INF/MANIFEST.MF

@@ -9,5 +9,7 @@ Import-Package: org.apache.tools.ant,
   org.eclipse.jgit.storage.file;version="[5.5.0,5.6.0)"
 Bundle-Localization: plugin
 Bundle-Vendor: %Bundle-Vendor
-Export-Package: org.eclipse.jgit.ant,
- org.eclipse.jgit.ant.tasks;version="5.5.0";uses:="org.apache.tools.ant.types,org.apache.tools.ant"
+Export-Package: org.eclipse.jgit.ant;version="5.5.0",
+ org.eclipse.jgit.ant.tasks;version="5.5.0";
+  uses:="org.apache.tools.ant,
+   org.apache.tools.ant.types"

org.eclipse.jgit.archive/META-INF/MANIFEST.MF

@@ -26,4 +26,4 @@ Export-Package: org.eclipse.jgit.archive;version="5.5.0";
    org.eclipse.jgit.api,
    org.apache.commons.compress.archivers,
    org.osgi.framework",
- org.eclipse.jgit.archive.internal;x-internal:=true
+ org.eclipse.jgit.archive.internal;version="5.5.0";x-internal:=true

org.eclipse.jgit.http.server/src/org/eclipse/jgit/http/server/FileSender.java

@@ -58,12 +58,14 @@ import java.io.IOException;
 import java.io.OutputStream;
 import java.io.RandomAccessFile;
 import java.text.MessageFormat;
+import java.time.Instant;
 import java.util.Enumeration;
 
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
 import org.eclipse.jgit.lib.ObjectId;
+import org.eclipse.jgit.util.FS;
 
 /**
  * Dumps a file over HTTP GET (or its information via HEAD).
@@ -76,7 +78,7 @@ final class FileSender {
 
 	private final RandomAccessFile source;
 
-	private final long lastModified;
+	private final Instant lastModified;
 
 	private final long fileLen;
 
@@ -89,7 +91,7 @@ final class FileSender {
 		this.source = new RandomAccessFile(path, "r");
 
 		try {
-			this.lastModified = path.lastModified();
+			this.lastModified = FS.DETECTED.lastModifiedInstant(path);
 			this.fileLen = source.getChannel().size();
 			this.end = fileLen;
 		} catch (IOException e) {
@@ -114,7 +116,7 @@ final class FileSender {
 		}
 	}
 
-	long getLastModified() {
+	Instant getLastModified() {
 		return lastModified;
 	}
 

org.eclipse.jgit.http.server/src/org/eclipse/jgit/http/server/ObjectFileServlet.java

@@ -54,6 +54,7 @@ import static org.eclipse.jgit.util.HttpSupport.HDR_LAST_MODIFIED;
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.IOException;
+import java.time.Instant;
 
 import javax.servlet.ServletException;
 import javax.servlet.http.HttpServlet;
@@ -76,7 +77,9 @@ abstract class ObjectFileServlet extends HttpServlet {
 
 		@Override
 		String etag(FileSender sender) throws IOException {
-			return Long.toHexString(sender.getLastModified());
+			Instant lastModified = sender.getLastModified();
+			return Long.toHexString(lastModified.getEpochSecond())
+					+ Long.toHexString(lastModified.getNano());
 		}
 	}
 
@@ -145,7 +148,9 @@ abstract class ObjectFileServlet extends HttpServlet {
 
 		try {
 			final String etag = etag(sender);
-			final long lastModified = (sender.getLastModified() / 1000) * 1000;
+			// HTTP header Last-Modified header has a resolution of 1 sec, see
+			// https://www.w3.org/Protocols/rfc2616/rfc2616-sec14.html#sec14.29
+			final long lastModified = sender.getLastModified().getEpochSecond();
 
 			String ifNoneMatch = req.getHeader(HDR_IF_NONE_MATCH);
 			if (etag != null && etag.equals(ifNoneMatch)) {

org.eclipse.jgit.junit/.settings/org.eclipse.jdt.core.prefs

@@ -1,10 +1,13 @@
 eclipse.preferences.version=1
-org.eclipse.jdt.core.compiler.annotation.inheritNullAnnotations=disabled
+org.eclipse.jdt.core.compiler.annotation.inheritNullAnnotations=enabled
 org.eclipse.jdt.core.compiler.annotation.missingNonNullByDefaultAnnotation=ignore
-org.eclipse.jdt.core.compiler.annotation.nonnull=org.eclipse.jdt.annotation.NonNull
-org.eclipse.jdt.core.compiler.annotation.nonnullbydefault=org.eclipse.jdt.annotation.NonNullByDefault
-org.eclipse.jdt.core.compiler.annotation.nullable=org.eclipse.jdt.annotation.Nullable
-org.eclipse.jdt.core.compiler.annotation.nullanalysis=disabled
+org.eclipse.jdt.core.compiler.annotation.nonnull=org.eclipse.jgit.annotations.NonNull
+org.eclipse.jdt.core.compiler.annotation.nonnull.secondary=
+org.eclipse.jdt.core.compiler.annotation.nonnullbydefault=org.eclipse.jgit.annotations.NonNullByDefault
+org.eclipse.jdt.core.compiler.annotation.nonnullbydefault.secondary=
+org.eclipse.jdt.core.compiler.annotation.nullable=org.eclipse.jgit.annotations.Nullable
+org.eclipse.jdt.core.compiler.annotation.nullable.secondary=
+org.eclipse.jdt.core.compiler.annotation.nullanalysis=enabled
 org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
 org.eclipse.jdt.core.compiler.codegen.methodParameters=do not generate
 org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8
@@ -14,6 +17,7 @@ org.eclipse.jdt.core.compiler.debug.lineNumber=generate
 org.eclipse.jdt.core.compiler.debug.localVariable=generate
 org.eclipse.jdt.core.compiler.debug.sourceFile=generate
 org.eclipse.jdt.core.compiler.doc.comment.support=enabled
+org.eclipse.jdt.core.compiler.problem.APILeak=warning
 org.eclipse.jdt.core.compiler.problem.annotationSuperInterface=warning
 org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
 org.eclipse.jdt.core.compiler.problem.autoboxing=warning
@@ -48,7 +52,7 @@ org.eclipse.jdt.core.compiler.problem.missingDefaultCase=ignore
 org.eclipse.jdt.core.compiler.problem.missingDeprecatedAnnotation=ignore
 org.eclipse.jdt.core.compiler.problem.missingEnumCaseDespiteDefault=disabled
 org.eclipse.jdt.core.compiler.problem.missingHashCodeMethod=error
-org.eclipse.jdt.core.compiler.problem.missingJavadocComments=ignore
+org.eclipse.jdt.core.compiler.problem.missingJavadocComments=error
 org.eclipse.jdt.core.compiler.problem.missingJavadocCommentsOverriding=disabled
 org.eclipse.jdt.core.compiler.problem.missingJavadocCommentsVisibility=protected
 org.eclipse.jdt.core.compiler.problem.missingJavadocTagDescription=return_tag
@@ -64,14 +68,16 @@ org.eclipse.jdt.core.compiler.problem.noEffectAssignment=error
 org.eclipse.jdt.core.compiler.problem.noImplicitStringConversion=error
 org.eclipse.jdt.core.compiler.problem.nonExternalizedStringLiteral=ignore
 org.eclipse.jdt.core.compiler.problem.nonnullParameterAnnotationDropped=warning
+org.eclipse.jdt.core.compiler.problem.nonnullTypeVariableFromLegacyInvocation=warning
 org.eclipse.jdt.core.compiler.problem.nullAnnotationInferenceConflict=error
 org.eclipse.jdt.core.compiler.problem.nullReference=error
 org.eclipse.jdt.core.compiler.problem.nullSpecViolation=error
-org.eclipse.jdt.core.compiler.problem.nullUncheckedConversion=warning
+org.eclipse.jdt.core.compiler.problem.nullUncheckedConversion=ignore
 org.eclipse.jdt.core.compiler.problem.overridingPackageDefaultMethod=warning
 org.eclipse.jdt.core.compiler.problem.parameterAssignment=ignore
+org.eclipse.jdt.core.compiler.problem.pessimisticNullAnalysisForFreeTypeVariables=warning
 org.eclipse.jdt.core.compiler.problem.possibleAccidentalBooleanAssignment=error
-org.eclipse.jdt.core.compiler.problem.potentialNullReference=warning
+org.eclipse.jdt.core.compiler.problem.potentialNullReference=error
 org.eclipse.jdt.core.compiler.problem.potentiallyUnclosedCloseable=ignore
 org.eclipse.jdt.core.compiler.problem.rawTypeReference=ignore
 org.eclipse.jdt.core.compiler.problem.redundantNullAnnotation=warning
@@ -86,16 +92,22 @@ org.eclipse.jdt.core.compiler.problem.suppressOptionalErrors=disabled
 org.eclipse.jdt.core.compiler.problem.suppressWarnings=enabled
 org.eclipse.jdt.core.compiler.problem.syntacticNullAnalysisForFields=disabled
 org.eclipse.jdt.core.compiler.problem.syntheticAccessEmulation=ignore
+org.eclipse.jdt.core.compiler.problem.terminalDeprecation=warning
 org.eclipse.jdt.core.compiler.problem.typeParameterHiding=warning
 org.eclipse.jdt.core.compiler.problem.unavoidableGenericTypeProblems=enabled
 org.eclipse.jdt.core.compiler.problem.uncheckedTypeOperation=warning
 org.eclipse.jdt.core.compiler.problem.unclosedCloseable=warning
 org.eclipse.jdt.core.compiler.problem.undocumentedEmptyBlock=warning
 org.eclipse.jdt.core.compiler.problem.unhandledWarningToken=ignore
+org.eclipse.jdt.core.compiler.problem.unhandledWarningToken=warning
+org.eclipse.jdt.core.compiler.problem.unlikelyCollectionMethodArgumentType=warning
+org.eclipse.jdt.core.compiler.problem.unlikelyCollectionMethodArgumentTypeStrict=disabled
+org.eclipse.jdt.core.compiler.problem.unlikelyEqualsArgumentType=info
 org.eclipse.jdt.core.compiler.problem.unnecessaryElse=ignore
 org.eclipse.jdt.core.compiler.problem.unnecessaryTypeCheck=error
 org.eclipse.jdt.core.compiler.problem.unqualifiedFieldAccess=ignore
-org.eclipse.jdt.core.compiler.problem.unusedDeclaredThrownException=error
+org.eclipse.jdt.core.compiler.problem.unstableAutoModuleName=warning
+org.eclipse.jdt.core.compiler.problem.unusedDeclaredThrownException=warning
 org.eclipse.jdt.core.compiler.problem.unusedDeclaredThrownExceptionExemptExceptionAndThrowable=enabled
 org.eclipse.jdt.core.compiler.problem.unusedDeclaredThrownExceptionIncludeDocCommentReference=enabled
 org.eclipse.jdt.core.compiler.problem.unusedDeclaredThrownExceptionWhenOverriding=disabled

org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/LocalDiskRepositoryTestCase.java

@@ -51,6 +51,8 @@ import static org.junit.Assert.fail;
 
 import java.io.File;
 import java.io.IOException;
+import java.io.PrintStream;
+import java.time.Instant;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.HashMap;
@@ -126,6 +128,10 @@ public abstract class LocalDiskRepositoryTestCase {
 		if (!tmp.delete() || !tmp.mkdir())
 			throw new IOException("Cannot create " + tmp);
 
+		// measure timer resolution before the test to avoid time critical tests
+		// are affected by time needed for measurement
+		FS.getFileStoreAttributes(tmp.toPath().getParent());
+
 		mockSystemReader = new MockSystemReader();
 		mockSystemReader.userGitConfig = new FileBasedConfig(new File(tmp,
 				"usergitconfig"), FS.DETECTED);
@@ -232,36 +238,30 @@ public abstract class LocalDiskRepositoryTestCase {
 	private static boolean recursiveDelete(final File dir,
 			boolean silent, boolean failOnError) {
 		assert !(silent && failOnError);
-		if (!dir.exists())
-			return silent;
-		final File[] ls = dir.listFiles();
-		if (ls != null) {
-			for (File f : ls) {
-				if (f.isDirectory()) {
-					silent = recursiveDelete(f, silent, failOnError);
-				} else if (!f.delete()) {
-					if (!silent) {
-						reportDeleteFailure(failOnError, f);
-					}
-					silent = !failOnError;
-				}
-			}
+		int options = FileUtils.RECURSIVE | FileUtils.RETRY
+				| FileUtils.SKIP_MISSING;
+		if (silent) {
+			options |= FileUtils.IGNORE_ERRORS;
 		}
-		if (!dir.delete()) {
-			if (!silent)
-				reportDeleteFailure(failOnError, dir);
-			silent = !failOnError;
+		try {
+			FileUtils.delete(dir, options);
+		} catch (IOException e) {
+			reportDeleteFailure(failOnError, dir, e);
+			return !failOnError;
 		}
-		return silent;
+		return true;
 	}
 
-	private static void reportDeleteFailure(boolean failOnError, File e) {
+	private static void reportDeleteFailure(boolean failOnError, File f,
+			Exception cause) {
 		String severity = failOnError ? "ERROR" : "WARNING";
-		String msg = severity + ": Failed to delete " + e;
-		if (failOnError)
+		String msg = severity + ": Failed to delete " + f;
+		if (failOnError) {
 			fail(msg);
-		else
+		} else {
 			System.err.println(msg);
+		}
+		cause.printStackTrace(new PrintStream(System.err));
 	}
 
 	/** Constant <code>MOD_TIME=1</code> */
@@ -323,12 +323,13 @@ public abstract class LocalDiskRepositoryTestCase {
 			throws IllegalStateException, IOException {
 		DirCache dc = repo.readDirCache();
 		StringBuilder sb = new StringBuilder();
-		TreeSet<Long> timeStamps = new TreeSet<>();
+		TreeSet<Instant> timeStamps = new TreeSet<>();
 
 		// iterate once over the dircache just to collect all time stamps
 		if (0 != (includedOptions & MOD_TIME)) {
-			for (int i=0; i<dc.getEntryCount(); ++i)
-				timeStamps.add(Long.valueOf(dc.getEntry(i).getLastModified()));
+			for (int i = 0; i < dc.getEntryCount(); ++i) {
+				timeStamps.add(dc.getEntry(i).getLastModifiedInstant());
+			}
 		}
 
 		// iterate again, now produce the result string
@@ -340,7 +341,8 @@ public abstract class LocalDiskRepositoryTestCase {
 				sb.append(", stage:" + stage);
 			if (0 != (includedOptions & MOD_TIME)) {
 				sb.append(", time:t"+
-						timeStamps.headSet(Long.valueOf(entry.getLastModified())).size());
+						timeStamps.headSet(entry.getLastModifiedInstant())
+								.size());
 			}
 			if (0 != (includedOptions & SMUDGE))
 				if (entry.isSmudged())

org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/Repeat.java

@@ -56,4 +56,13 @@ public @interface Repeat {
 	 * Number of repetitions
 	 */
 	public abstract int n();
+
+	/**
+	 * Whether to abort execution on first test failure
+	 *
+	 * @return {@code true} if execution should be aborted on the first failure,
+	 *         otherwise count failures and continue execution
+	 * @since 5.1.9
+	 */
+	public boolean abortOnFailure() default true;
 }

org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/RepeatRule.java

@@ -81,9 +81,31 @@ public class RepeatRule implements TestRule {
 	private static Logger LOG = Logger
 			.getLogger(RepeatRule.class.getName());
 
+	/**
+	 * Exception thrown if repeated execution of a test annotated with
+	 * {@code @Repeat} failed.
+	 */
 	public static class RepeatedTestException extends RuntimeException {
 		private static final long serialVersionUID = 1L;
 
+		/**
+		 * Constructor
+		 *
+		 * @param message
+		 *            the error message
+		 */
+		public RepeatedTestException(String message) {
+			super(message);
+		}
+
+		/**
+		 * Constructor
+		 *
+		 * @param message
+		 *            the error message
+		 * @param cause
+		 *            exception causing this exception
+		 */
 		public RepeatedTestException(String message, Throwable cause) {
 			super(message, cause);
 		}
@@ -93,28 +115,45 @@ public class RepeatRule implements TestRule {
 
 		private final int repetitions;
 
+		private boolean abortOnFailure;
+
 		private final Statement statement;
 
-		private RepeatStatement(int repetitions, Statement statement) {
+		private RepeatStatement(int repetitions, boolean abortOnFailure,
+				Statement statement) {
 			this.repetitions = repetitions;
+			this.abortOnFailure = abortOnFailure;
 			this.statement = statement;
 		}
 
 		@Override
 		public void evaluate() throws Throwable {
+			int failures = 0;
 			for (int i = 0; i < repetitions; i++) {
 				try {
 					statement.evaluate();
 				} catch (Throwable e) {
+					failures += 1;
 					RepeatedTestException ex = new RepeatedTestException(
 							MessageFormat.format(
 									"Repeated test failed when run for the {0}. time",
 									Integer.valueOf(i + 1)),
 							e);
 					LOG.log(Level.SEVERE, ex.getMessage(), ex);
-					throw ex;
+					if (abortOnFailure) {
+						throw ex;
+					}
 				}
 			}
+			if (failures > 0) {
+				RepeatedTestException e = new RepeatedTestException(
+						MessageFormat.format(
+								"Test failed {0} times out of {1} repeated executions",
+								Integer.valueOf(failures),
+								Integer.valueOf(repetitions)));
+				LOG.log(Level.SEVERE, e.getMessage(), e);
+				throw e;
+			}
 		}
 	}
 
@@ -125,7 +164,8 @@ public class RepeatRule implements TestRule {
 		Repeat repeat = description.getAnnotation(Repeat.class);
 		if (repeat != null) {
 			int n = repeat.n();
-			result = new RepeatStatement(n, statement);
+			boolean abortOnFailure = repeat.abortOnFailure();
+			result = new RepeatStatement(n, abortOnFailure, statement);
 		}
 		return result;
 	}

org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/RepositoryTestCase.java

@@ -57,7 +57,9 @@ import java.io.IOException;
 import java.io.InputStreamReader;
 import java.io.Reader;
 import java.nio.file.Path;
+import java.time.Instant;
 import java.util.Map;
+import java.util.concurrent.TimeUnit;
 
 import org.eclipse.jgit.api.Git;
 import org.eclipse.jgit.api.errors.GitAPIException;
@@ -284,7 +286,7 @@ public abstract class RepositoryTestCase extends LocalDiskRepositoryTestCase {
 
 				dce = new DirCacheEntry(treeItr.getEntryPathString());
 				dce.setFileMode(treeItr.getEntryFileMode());
-				dce.setLastModified(treeItr.getEntryLastModified());
+				dce.setLastModified(treeItr.getEntryLastModifiedInstant());
 				dce.setLength((int) len);
 				try (FileInputStream in = new FileInputStream(
 						treeItr.getEntryFile())) {
@@ -361,7 +363,8 @@ public abstract class RepositoryTestCase extends LocalDiskRepositoryTestCase {
 	 * @throws InterruptedException
 	 * @throws IOException
 	 */
-	public static long fsTick(File lastFile) throws InterruptedException,
+	public static Instant fsTick(File lastFile)
+			throws InterruptedException,
 			IOException {
 		File tmp;
 		FS fs = FS.DETECTED;
@@ -375,15 +378,16 @@ public abstract class RepositoryTestCase extends LocalDiskRepositoryTestCase {
 			tmp = File.createTempFile("fsTickTmpFile", null,
 					lastFile.getParentFile());
 		}
-		long res = FS.getFsTimerResolution(tmp.toPath()).toMillis();
+		long res = FS.getFileStoreAttributes(tmp.toPath())
+				.getFsTimestampResolution().toNanos();
 		long sleepTime = res / 10;
 		try {
-			long startTime = fs.lastModified(lastFile);
-			long actTime = fs.lastModified(tmp);
-			while (actTime <= startTime) {
-				Thread.sleep(sleepTime);
+			Instant startTime = fs.lastModifiedInstant(lastFile);
+			Instant actTime = fs.lastModifiedInstant(tmp);
+			while (actTime.compareTo(startTime) <= 0) {
+				TimeUnit.NANOSECONDS.sleep(sleepTime);
 				FileUtils.touch(tmp.toPath());
-				actTime = fs.lastModified(tmp);
+				actTime = fs.lastModifiedInstant(tmp);
 			}
 			return actTime;
 		} finally {

org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/TestRepository.java

@@ -728,7 +728,7 @@ public class TestRepository<R extends Repository> implements AutoCloseable {
 		ThreeWayMerger merger = MergeStrategy.RECURSIVE.newMerger(db, true);
 		merger.setBase(parent.getTree());
 		if (merger.merge(head, commit)) {
-			if (AnyObjectId.equals(head.getTree(), merger.getResultTreeId()))
+			if (AnyObjectId.isEqual(head.getTree(), merger.getResultTreeId()))
 				return null;
 			tick(1);
 			org.eclipse.jgit.lib.CommitBuilder b =
@@ -1076,6 +1076,14 @@ public class TestRepository<R extends Repository> implements AutoCloseable {
 			parents.add(prior.create());
 		}
 
+		/**
+		 * set parent commit
+		 *
+		 * @param p
+		 *            parent commit
+		 * @return this commit builder
+		 * @throws Exception
+		 */
 		public CommitBuilder parent(RevCommit p) throws Exception {
 			if (parents.isEmpty()) {
 				DirCacheBuilder b = tree.builder();
@@ -1088,29 +1096,71 @@ public class TestRepository<R extends Repository> implements AutoCloseable {
 			return this;
 		}
 
+		/**
+		 * Get parent commits
+		 *
+		 * @return parent commits
+		 */
 		public List<RevCommit> parents() {
 			return Collections.unmodifiableList(parents);
 		}
 
+		/**
+		 * Remove parent commits
+		 *
+		 * @return this commit builder
+		 */
 		public CommitBuilder noParents() {
 			parents.clear();
 			return this;
 		}
 
+		/**
+		 * Remove files
+		 *
+		 * @return this commit builder
+		 */
 		public CommitBuilder noFiles() {
 			tree.clear();
 			return this;
 		}
 
+		/**
+		 * Set top level tree
+		 *
+		 * @param treeId
+		 *            the top level tree
+		 * @return this commit builder
+		 */
 		public CommitBuilder setTopLevelTree(ObjectId treeId) {
 			topLevelTree = treeId;
 			return this;
 		}
 
+		/**
+		 * Add file with given content
+		 *
+		 * @param path
+		 *            path of the file
+		 * @param content
+		 *            the file content
+		 * @return this commit builder
+		 * @throws Exception
+		 */
 		public CommitBuilder add(String path, String content) throws Exception {
 			return add(path, blob(content));
 		}
 
+		/**
+		 * Add file with given path and blob
+		 *
+		 * @param path
+		 *            path of the file
+		 * @param id
+		 *            blob for this file
+		 * @return this commit builder
+		 * @throws Exception
+		 */
 		public CommitBuilder add(String path, RevBlob id)
 				throws Exception {
 			return edit(new PathEdit(path) {
@@ -1122,6 +1172,13 @@ public class TestRepository<R extends Repository> implements AutoCloseable {
 			});
 		}
 
+		/**
+		 * Edit the index
+		 *
+		 * @param edit
+		 *            the index record update
+		 * @return this commit builder
+		 */
 		public CommitBuilder edit(PathEdit edit) {
 			DirCacheEditor e = tree.editor();
 			e.add(edit);
@@ -1129,6 +1186,13 @@ public class TestRepository<R extends Repository> implements AutoCloseable {
 			return this;
 		}
 
+		/**
+		 * Remove a file
+		 *
+		 * @param path
+		 *            path of the file
+		 * @return this commit builder
+		 */
 		public CommitBuilder rm(String path) {
 			DirCacheEditor e = tree.editor();
 			e.add(new DeletePath(path));
@@ -1137,49 +1201,111 @@ public class TestRepository<R extends Repository> implements AutoCloseable {
 			return this;
 		}
 
+		/**
+		 * Set commit message
+		 *
+		 * @param m
+		 *            the message
+		 * @return this commit builder
+		 */
 		public CommitBuilder message(String m) {
 			message = m;
 			return this;
 		}
 
+		/**
+		 * Get the commit message
+		 *
+		 * @return the commit message
+		 */
 		public String message() {
 			return message;
 		}
 
+		/**
+		 * Tick the clock
+		 *
+		 * @param secs
+		 *            number of seconds
+		 * @return this commit builder
+		 */
 		public CommitBuilder tick(int secs) {
 			tick = secs;
 			return this;
 		}
 
+		/**
+		 * Set author and committer identity
+		 *
+		 * @param ident
+		 *            identity to set
+		 * @return this commit builder
+		 */
 		public CommitBuilder ident(PersonIdent ident) {
 			author = ident;
 			committer = ident;
 			return this;
 		}
 
+		/**
+		 * Set the author identity
+		 *
+		 * @param a
+		 *            the author's identity
+		 * @return this commit builder
+		 */
 		public CommitBuilder author(PersonIdent a) {
 			author = a;
 			return this;
 		}
 
+		/**
+		 * Get the author identity
+		 *
+		 * @return the author identity
+		 */
 		public PersonIdent author() {
 			return author;
 		}
 
+		/**
+		 * Set the committer identity
+		 *
+		 * @param c
+		 *            the committer identity
+		 * @return this commit builder
+		 */
 		public CommitBuilder committer(PersonIdent c) {
 			committer = c;
 			return this;
 		}
 
+		/**
+		 * Get the committer identity
+		 *
+		 * @return the committer identity
+		 */
 		public PersonIdent committer() {
 			return committer;
 		}
 
+		/**
+		 * Insert changeId
+		 *
+		 * @return this commit builder
+		 */
 		public CommitBuilder insertChangeId() {
 			changeId = "";
 			return this;
 		}
 
+		/**
+		 * Insert given changeId
+		 *
+		 * @param c
+		 *            changeId
+		 * @return this commit builder
+		 */
 		public CommitBuilder insertChangeId(String c) {
 			// Validate, but store as a string so we can use "" as a sentinel.
 			ObjectId.fromString(c);
@@ -1187,6 +1313,13 @@ public class TestRepository<R extends Repository> implements AutoCloseable {
 			return this;
 		}
 
+		/**
+		 * Create the commit
+		 *
+		 * @return the new commit
+		 * @throws Exception
+		 *             if creation failed
+		 */
 		public RevCommit create() throws Exception {
 			if (self == null) {
 				TestRepository.this.tick(tick);
@@ -1247,6 +1380,12 @@ public class TestRepository<R extends Repository> implements AutoCloseable {
 						+ cid.getName() + "\n"); //$NON-NLS-1$
 		}
 
+		/**
+		 * Create child commit builder
+		 *
+		 * @return child commit builder
+		 * @throws Exception
+		 */
 		public CommitBuilder child() throws Exception {
 			return new CommitBuilder(this);
 		}

org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/time/TimeUtil.java

@@ -0,0 +1,99 @@
+/*
+ * Copyright (C) 2019, Matthias Sohn <matthias.sohn@sap.com>
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+package org.eclipse.jgit.junit.time;
+
+import java.io.IOException;
+import java.io.UncheckedIOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.attribute.FileTime;
+import java.time.Instant;
+
+import org.eclipse.jgit.util.FS;
+
+/**
+ * Utility methods for handling timestamps
+ */
+public class TimeUtil {
+	/**
+	 * Set the lastModified time of a given file by adding a given offset to the
+	 * current lastModified time
+	 *
+	 * @param path
+	 *            path of a file to set last modified
+	 * @param offsetMillis
+	 *            offset in milliseconds, if negative the new lastModified time
+	 *            is offset before the original lastModified time, otherwise
+	 *            after the original time
+	 * @return the new lastModified time
+	 */
+	public static Instant setLastModifiedWithOffset(Path path,
+			long offsetMillis) {
+		Instant mTime = FS.DETECTED.lastModifiedInstant(path)
+				.plusMillis(offsetMillis);
+		try {
+			Files.setLastModifiedTime(path, FileTime.from(mTime));
+			return mTime;
+		} catch (IOException e) {
+			throw new UncheckedIOException(e);
+		}
+	}
+
+	/**
+	 * Set the lastModified time of file a to the one from file b
+	 *
+	 * @param a
+	 *            file to set lastModified time
+	 * @param b
+	 *            file to read lastModified time from
+	 */
+	public static void setLastModifiedOf(Path a, Path b) {
+		Instant mTime = FS.DETECTED.lastModifiedInstant(b);
+		try {
+			Files.setLastModifiedTime(a, FileTime.from(mTime));
+		} catch (IOException e) {
+			throw new UncheckedIOException(e);
+		}
+	}
+
+}

org.eclipse.jgit.lfs.server.test/tst/org/eclipse/jgit/lfs/server/fs/LfsServerTest.java

@@ -82,6 +82,7 @@ import org.eclipse.jgit.lfs.lib.LongObjectId;
 import org.eclipse.jgit.lfs.server.LargeFileRepository;
 import org.eclipse.jgit.lfs.server.LfsProtocolServlet;
 import org.eclipse.jgit.lfs.test.LongObjectIdTestUtils;
+import org.eclipse.jgit.util.FS;
 import org.eclipse.jgit.util.FileUtils;
 import org.eclipse.jgit.util.IO;
 import org.junit.After;
@@ -119,6 +120,11 @@ public abstract class LfsServerTest {
 	@Before
 	public void setup() throws Exception {
 		tmp = Files.createTempDirectory("jgit_test_");
+
+		// measure timer resolution before the test to avoid time critical tests
+		// are affected by time needed for measurement
+		FS.getFileStoreAttributes(tmp.getParent());
+
 		server = new AppServer();
 		ServletContextHandler app = server.addContext("/lfs");
 		dir = Paths.get(tmp.toString(), "lfs");

org.eclipse.jgit.lfs/.settings/.api_filters

@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<component id="org.eclipse.jgit.lfs" version="2">
+    <resource path="src/org/eclipse/jgit/lfs/lib/AnyLongObjectId.java" type="org.eclipse.jgit.lfs.lib.AnyLongObjectId">
+        <filter id="1141899266">
+            <message_arguments>
+                <message_argument value="5.4"/>
+                <message_argument value="5.5"/>
+                <message_argument value="isEqual(AnyLongObjectId, AnyLongObjectId)"/>
+            </message_arguments>
+        </filter>
+    </resource>
+</component>

org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/lib/AnyLongObjectId.java

@@ -50,6 +50,7 @@ import java.nio.ByteBuffer;
 
 import org.eclipse.jgit.lib.AnyObjectId;
 import org.eclipse.jgit.util.NB;
+import org.eclipse.jgit.util.References;
 
 /**
  * A (possibly mutable) SHA-256 abstraction.
@@ -73,11 +74,31 @@ public abstract class AnyLongObjectId implements Comparable<AnyLongObjectId> {
 	 * @param secondObjectId
 	 *            the second identifier to compare. Must not be null.
 	 * @return true if the two identifiers are the same.
+	 * @deprecated use {@link #isEqual(AnyLongObjectId, AnyLongObjectId)}
+	 *             instead.
 	 */
+	@Deprecated
+	@SuppressWarnings("AmbiguousMethodReference")
 	public static boolean equals(final AnyLongObjectId firstObjectId,
 			final AnyLongObjectId secondObjectId) {
-		if (firstObjectId == secondObjectId)
+		return isEqual(firstObjectId, secondObjectId);
+	}
+
+	/**
+	 * Compare two object identifier byte sequences for equality.
+	 *
+	 * @param firstObjectId
+	 *            the first identifier to compare. Must not be null.
+	 * @param secondObjectId
+	 *            the second identifier to compare. Must not be null.
+	 * @return true if the two identifiers are the same.
+	 * @since 5.4
+	 */
+	public static boolean isEqual(final AnyLongObjectId firstObjectId,
+			final AnyLongObjectId secondObjectId) {
+		if (References.isSameObject(firstObjectId, secondObjectId)) {
 			return true;
+		}
 
 		// We test word 2 first as odds are someone already used our
 		// word 1 as a hash code, and applying that came up with these
@@ -274,6 +295,7 @@ public abstract class AnyLongObjectId implements Comparable<AnyLongObjectId> {
 	 *            the other id to compare to. May be null.
 	 * @return true only if both LongObjectIds have identical bits.
 	 */
+	@SuppressWarnings({ "NonOverridingEquals", "AmbiguousMethodReference" })
 	public final boolean equals(AnyLongObjectId other) {
 		return other != null ? equals(this, other) : false;
 	}

org.eclipse.jgit.packaging/pom.xml

@@ -47,10 +47,6 @@
     xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
   <modelVersion>4.0.0</modelVersion>
 
-  <prerequisites>
-    <maven>3.0</maven>
-  </prerequisites>
-
   <groupId>org.eclipse.jgit</groupId>
   <artifactId>jgit.tycho.parent</artifactId>
   <version>5.5.0-SNAPSHOT</version>
@@ -289,6 +285,21 @@
           <artifactId>tycho-p2-plugin</artifactId>
           <version>${tycho-version}</version>
         </plugin>
+        <plugin>
+          <groupId>org.eclipse.tycho</groupId>
+          <artifactId>tycho-p2-publisher-plugin</artifactId>
+          <version>${tycho-version}</version>
+        </plugin>
+        <plugin>
+          <groupId>org.eclipse.tycho</groupId>
+          <artifactId>tycho-p2-repository-plugin</artifactId>
+          <version>${tycho-version}</version>
+        </plugin>
+        <plugin>
+          <groupId>org.eclipse.tycho</groupId>
+          <artifactId>tycho-packaging-plugin</artifactId>
+          <version>${tycho-version}</version>
+        </plugin>
         <plugin>
           <groupId>org.eclipse.tycho.extras</groupId>
           <artifactId>tycho-pack200a-plugin</artifactId>
@@ -309,6 +320,25 @@
           <artifactId>build-helper-maven-plugin</artifactId>
           <version>3.0.0</version>
         </plugin>
+        <plugin>
+          <artifactId>maven-clean-plugin</artifactId>
+          <version>3.1.0</version>
+        </plugin>
+        <plugin>
+          <groupId>org.apache.maven.plugins</groupId>
+          <artifactId>maven-deploy-plugin</artifactId>
+          <version>3.0.0-M1</version>
+        </plugin>
+        <plugin>
+          <groupId>org.apache.maven.plugins</groupId>
+          <artifactId>maven-install-plugin</artifactId>
+          <version>3.0.0-M1</version>
+        </plugin>
+        <plugin>
+          <groupId>org.apache.maven.plugins</groupId>
+          <artifactId>maven-site-plugin</artifactId>
+          <version>3.7.1</version>
+        </plugin>
       </plugins>
     </pluginManagement>
   </build>

org.eclipse.jgit.pgm/pom.xml

@@ -142,6 +142,12 @@
       <artifactId>org.eclipse.jgit.lfs.server</artifactId>
       <version>${project.version}</version>
     </dependency>
+
+    <dependency>
+      <groupId>org.tukaani</groupId>
+      <artifactId>xz</artifactId>
+      <optional>true</optional>
+    </dependency>
   </dependencies>
 
   <build>

org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Blame.java

@@ -218,7 +218,8 @@ class Blame extends TextBuiltin {
 					dateWidth = Math.max(dateWidth, date(line).length());
 					pathWidth = Math.max(pathWidth, path(line).length());
 				}
-				while (line + 1 < end && blame.getSourceCommit(line + 1) == c) {
+				while (line + 1 < end
+						&& sameCommit(blame.getSourceCommit(line + 1), c)) {
 					line++;
 				}
 				maxSourceLine = Math.max(maxSourceLine, blame.getSourceLine(line));
@@ -257,13 +258,22 @@ class Blame extends TextBuiltin {
 					blame.getResultContents().writeLine(outs, line);
 					outs.flush();
 					outw.print('\n');
-				} while (++line < end && blame.getSourceCommit(line) == c);
+				} while (++line < end
+						&& sameCommit(blame.getSourceCommit(line), c));
 			}
 		} catch (NoWorkTreeException | IOException e) {
 			throw die(e.getMessage(), e);
 		}
 	}
 
+	@SuppressWarnings("ReferenceEquality")
+	private static boolean sameCommit(RevCommit a, RevCommit b) {
+		// Reference comparison is intentional; BlameGenerator uses a single
+		// RevWalk which caches the RevCommit objects, and if a given commit
+		// is cached the RevWalk returns the same instance.
+		return a == b;
+	}
+
 	private int uniqueAbbrevLen(ObjectReader reader, RevCommit commit)
 			throws IOException {
 		return reader.abbreviate(commit, abbrev).length();

org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/TextBuiltin.java

@@ -45,8 +45,8 @@
 package org.eclipse.jgit.pgm;
 
 import static java.nio.charset.StandardCharsets.UTF_8;
-import static org.eclipse.jgit.lib.ConfigConstants.CONFIG_SECTION_I18N;
 import static org.eclipse.jgit.lib.ConfigConstants.CONFIG_KEY_LOG_OUTPUT_ENCODING;
+import static org.eclipse.jgit.lib.ConfigConstants.CONFIG_SECTION_I18N;
 import static org.eclipse.jgit.lib.Constants.R_HEADS;
 import static org.eclipse.jgit.lib.Constants.R_REMOTES;
 import static org.eclipse.jgit.lib.Constants.R_TAGS;

org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/ShowDirCache.java

@@ -48,8 +48,10 @@ package org.eclipse.jgit.pgm.debug;
 
 import static java.lang.Integer.valueOf;
 
-import java.text.SimpleDateFormat;
-import java.util.Date;
+import java.time.Instant;
+import java.time.ZoneId;
+import java.time.format.DateTimeFormatter;
+import java.util.Locale;
 
 import org.eclipse.jgit.dircache.DirCache;
 import org.eclipse.jgit.dircache.DirCacheEntry;
@@ -67,25 +69,27 @@ class ShowDirCache extends TextBuiltin {
 	/** {@inheritDoc} */
 	@Override
 	protected void run() throws Exception {
-		final SimpleDateFormat fmt;
-		fmt = new SimpleDateFormat("yyyy-MM-dd,HH:mm:ss.SSS"); //$NON-NLS-1$
+		final DateTimeFormatter fmt = DateTimeFormatter
+				.ofPattern("yyyy-MM-dd,HH:mm:ss.nnnnnnnnn") //$NON-NLS-1$
+				.withLocale(Locale.getDefault())
+				.withZone(ZoneId.systemDefault());
 
 		final DirCache cache = db.readDirCache();
 		for (int i = 0; i < cache.getEntryCount(); i++) {
 			final DirCacheEntry ent = cache.getEntry(i);
 			final FileMode mode = FileMode.fromBits(ent.getRawMode());
 			final int len = ent.getLength();
-			long lastModified = ent.getLastModified();
-			final Date mtime = new Date(lastModified);
+			Instant mtime = ent.getLastModifiedInstant();
 			final int stage = ent.getStage();
 
 			outw.print(mode);
 			outw.format(" %6d", valueOf(len)); //$NON-NLS-1$
 			outw.print(' ');
-			if (millis)
-				outw.print(lastModified);
-			else
+			if (millis) {
+				outw.print(mtime.toEpochMilli());
+			} else {
 				outw.print(fmt.format(mtime));
+			}
 			outw.print(' ');
 			outw.print(ent.getObjectId().name());
 			outw.print(' ');

org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/VerifyReftable.java

@@ -189,7 +189,7 @@ class VerifyReftable extends TextBuiltin {
 			return;
 		}
 
-		if (!AnyObjectId.equals(exp.getObjectId(), act.getObjectId())) {
+		if (!AnyObjectId.isEqual(exp.getObjectId(), act.getObjectId())) {
 			throw die(String.format("expected %s to be %s, found %s",
 					exp.getName(),
 					id(exp.getObjectId()),
@@ -197,7 +197,8 @@ class VerifyReftable extends TextBuiltin {
 		}
 
 		if (exp.getPeeledObjectId() != null
-				&& !AnyObjectId.equals(exp.getPeeledObjectId(), act.getPeeledObjectId())) {
+				&& !AnyObjectId.isEqual(exp.getPeeledObjectId(),
+						act.getPeeledObjectId())) {
 			throw die(String.format("expected %s to be %s, found %s",
 					exp.getName(),
 					id(exp.getPeeledObjectId()),

org.eclipse.jgit.test/BUILD

@@ -24,7 +24,6 @@ HELPERS = glob(
     "revwalk/RevWalkTestCase.java",
     "transport/ObjectIdMatcher.java",
     "transport/SpiTransport.java",
-    "treewalk/FileTreeIteratorWithTimeControl.java",
     "treewalk/filter/AlwaysCloneTreeFilter.java",
     "test/resources/SampleDataRepositoryTestCase.java",
     "util/CPUTimeStopWatch.java",

org.eclipse.jgit.test/META-INF/MANIFEST.MF

@@ -11,10 +11,17 @@ Bundle-RequiredExecutionEnvironment: JavaSE-1.8
 Import-Package: com.googlecode.javaewah;version="[1.1.6,2.0.0)",
  com.jcraft.jsch;version="[0.1.54,0.2.0)",
  net.bytebuddy.dynamic.loading;version="[1.7.0,2.0.0)",
+ org.apache.commons.compress.archivers;version="[1.15.0,2.0)",
+ org.apache.commons.compress.archivers.tar;version="[1.15.0,2.0)",
+ org.apache.commons.compress.archivers.zip;version="[1.15.0,2.0)",
+ org.apache.commons.compress.compressors.bzip2;version="[1.15.0,2.0)",
+ org.apache.commons.compress.compressors.gzip;version="[1.15.0,2.0)",
+ org.apache.commons.compress.compressors.xz;version="[1.15.0,2.0)",
  org.bouncycastle.util.encoders;version="[1.61.0,2.0.0)",
  org.eclipse.jgit.annotations;version="[5.5.0,5.6.0)",
  org.eclipse.jgit.api;version="[5.5.0,5.6.0)",
  org.eclipse.jgit.api.errors;version="[5.5.0,5.6.0)",
+ org.eclipse.jgit.archive;version="[5.5.0,5.6.0)",
  org.eclipse.jgit.attributes;version="[5.5.0,5.6.0)",
  org.eclipse.jgit.awtui;version="[5.5.0,5.6.0)",
  org.eclipse.jgit.blame;version="[5.5.0,5.6.0)",
@@ -39,6 +46,7 @@ Import-Package: com.googlecode.javaewah;version="[1.1.6,2.0.0)",
  org.eclipse.jgit.internal.transport.parser;version="[5.5.0,5.6.0)",
  org.eclipse.jgit.junit;version="[5.5.0,5.6.0)",
  org.eclipse.jgit.junit.ssh;version="[5.5.0,5.6.0)",
+ org.eclipse.jgit.junit.time;version="[5.5.0,5.6.0)",
  org.eclipse.jgit.lfs;version="[5.5.0,5.6.0)",
  org.eclipse.jgit.lib;version="[5.5.0,5.6.0)",
  org.eclipse.jgit.merge;version="[5.5.0,5.6.0)",
@@ -71,7 +79,8 @@ Import-Package: com.googlecode.javaewah;version="[1.1.6,2.0.0)",
  org.mockito.junit;version="[2.13.0,3.0.0)",
  org.mockito.stubbing;version="[2.13.0,3.0.0)",
  org.objenesis;version="[2.6.0,3.0.0)",
- org.slf4j;version="[1.7.0,2.0.0)"
+ org.slf4j;version="[1.7.0,2.0.0)",
+ org.tukaani.xz;version="[1.6.0,2.0)"
 Require-Bundle: org.hamcrest.core;bundle-version="[1.1.0,2.0.0)",
  org.hamcrest.library;bundle-version="[1.1.0,2.0.0)"
 Export-Package: org.eclipse.jgit.transport.ssh;version="5.5.0";x-friends:="org.eclipse.jgit.ssh.apache.test"

org.eclipse.jgit.test/pom.xml

@@ -133,6 +133,12 @@
       <artifactId>org.eclipse.jgit.pgm</artifactId>
       <version>${project.version}</version>
     </dependency>
+
+    <dependency>
+      <groupId>org.tukaani</groupId>
+      <artifactId>xz</artifactId>
+      <optional>true</optional>
+    </dependency>
   </dependencies>
 
   <profiles>
@@ -144,6 +150,7 @@
           <plugin>
             <groupId>org.apache.maven.plugins</groupId>
             <artifactId>maven-surefire-plugin</artifactId>
+            <version>${maven-surefire-plugin-version}</version>
             <configuration>
               <argLine>@{argLine} -Djgit.test.long=true</argLine>
             </configuration>

org.eclipse.jgit.test/tests.bzl

@@ -58,6 +58,12 @@ def tests(tests):
             additional_deps = [
                 "//lib:mockito",
             ]
+        if src.endswith("ArchiveCommandTest.java"):
+            additional_deps = [
+                "//lib:commons-compress",
+                "//lib:xz",
+                "//org.eclipse.jgit.archive:jgit-archive",
+            ]
         heap_size = "-Xmx256m"
         if src.endswith("HugeCommitMessageTest.java"):
             heap_size = "-Xmx512m"

org.eclipse.jgit.test/tst-rsrc/log4j.properties

@@ -7,3 +7,8 @@ log4j.appender.stdout=org.apache.log4j.ConsoleAppender
 log4j.appender.stdout.Target=System.out
 log4j.appender.stdout.layout=org.apache.log4j.PatternLayout
 log4j.appender.stdout.layout.ConversionPattern=%d{yyyy-MM-dd HH:mm:ss} %-5p %c{1}:%L - %m%n
+#log4j.appender.fileLogger.bufferedIO = true
+#log4j.appender.fileLogger.bufferSize = 4096
+
+#log4j.logger.org.eclipse.jgit.util.FS = DEBUG
+#log4j.logger.org.eclipse.jgit.internal.storage.file.FileSnapshot = DEBUG

org.eclipse.jgit.test/tst/org/eclipse/jgit/api/AddCommandTest.java

@@ -1267,7 +1267,7 @@ public class AddCommandTest extends RepositoryTestCase {
 		DirCacheEntry entry = new DirCacheEntry(path, stage);
 		entry.setObjectId(id);
 		entry.setFileMode(FileMode.REGULAR_FILE);
-		entry.setLastModified(file.lastModified());
+		entry.setLastModified(FS.DETECTED.lastModifiedInstant(file));
 		entry.setLength((int) file.length());
 
 		builder.add(entry);

org.eclipse.jgit.test/tst/org/eclipse/jgit/api/ArchiveCommandTest.java

@@ -47,20 +47,44 @@ import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertNull;
 
 import java.beans.Statement;
+import java.io.BufferedInputStream;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
 import java.io.IOException;
+import java.io.InputStream;
 import java.io.OutputStream;
+import java.nio.file.Files;
 import java.util.Arrays;
 import java.util.Collections;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
+import org.apache.commons.compress.archivers.ArchiveEntry;
+import org.apache.commons.compress.archivers.ArchiveInputStream;
+import org.apache.commons.compress.archivers.tar.TarArchiveInputStream;
+import org.apache.commons.compress.archivers.zip.ZipArchiveInputStream;
+import org.apache.commons.compress.compressors.bzip2.BZip2CompressorInputStream;
+import org.apache.commons.compress.compressors.gzip.GzipCompressorInputStream;
+import org.apache.commons.compress.compressors.xz.XZCompressorInputStream;
+import org.eclipse.jgit.api.errors.AbortedByHookException;
+import org.eclipse.jgit.api.errors.ConcurrentRefUpdateException;
 import org.eclipse.jgit.api.errors.GitAPIException;
+import org.eclipse.jgit.api.errors.NoFilepatternException;
+import org.eclipse.jgit.api.errors.NoHeadException;
+import org.eclipse.jgit.api.errors.NoMessageException;
+import org.eclipse.jgit.api.errors.UnmergedPathsException;
+import org.eclipse.jgit.api.errors.WrongRepositoryStateException;
+import org.eclipse.jgit.archive.ArchiveFormats;
+import org.eclipse.jgit.errors.AmbiguousObjectException;
+import org.eclipse.jgit.errors.IncorrectObjectTypeException;
 import org.eclipse.jgit.junit.RepositoryTestCase;
 import org.eclipse.jgit.lib.FileMode;
 import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.lib.ObjectLoader;
 import org.eclipse.jgit.revwalk.RevCommit;
+import org.eclipse.jgit.util.IO;
 import org.eclipse.jgit.util.StringUtils;
 import org.junit.After;
 import org.junit.Before;
@@ -68,9 +92,14 @@ import org.junit.Test;
 
 public class ArchiveCommandTest extends RepositoryTestCase {
 
+	// archives store timestamp with 1 second resolution
+	private static final int WAIT = 2000;
 	private static final String UNEXPECTED_ARCHIVE_SIZE  = "Unexpected archive size";
 	private static final String UNEXPECTED_FILE_CONTENTS = "Unexpected file contents";
 	private static final String UNEXPECTED_TREE_CONTENTS = "Unexpected tree contents";
+	private static final String UNEXPECTED_LAST_MODIFIED =
+			"Unexpected lastModified mocked by MockSystemReader, truncated to 1 second";
+	private static final String UNEXPECTED_DIFFERENT_HASH = "Unexpected different hash";
 
 	private MockFormat format = null;
 
@@ -78,25 +107,20 @@ public class ArchiveCommandTest extends RepositoryTestCase {
 	public void setup() {
 		format = new MockFormat();
 		ArchiveCommand.registerFormat(format.SUFFIXES.get(0), format);
+		ArchiveFormats.registerAll();
 	}
 
 	@Override
 	@After
 	public void tearDown() {
 		ArchiveCommand.unregisterFormat(format.SUFFIXES.get(0));
+		ArchiveFormats.unregisterAll();
 	}
 
 	@Test
 	public void archiveHeadAllFiles() throws IOException, GitAPIException {
 		try (Git git = new Git(db)) {
-			writeTrashFile("file_1.txt", "content_1_1");
-			git.add().addFilepattern("file_1.txt").call();
-			git.commit().setMessage("create file").call();
-
-			writeTrashFile("file_1.txt", "content_1_2");
-			writeTrashFile("file_2.txt", "content_2_2");
-			git.add().addFilepattern(".").call();
-			git.commit().setMessage("updated file").call();
+			createTestContent(git);
 
 			git.archive().setOutputStream(new MockOutputStream())
 					.setFormat(format.SUFFIXES.get(0))
@@ -191,6 +215,157 @@ public class ArchiveCommandTest extends RepositoryTestCase {
 		}
 	}
 
+	@Test
+	public void archiveHeadAllFilesTarTimestamps() throws Exception {
+		try (Git git = new Git(db)) {
+			createTestContent(git);
+			String fmt = "tar";
+			File archive = new File(getTemporaryDirectory(),
+					"archive." + format);
+			archive(git, archive, fmt);
+			ObjectId hash1 = ObjectId.fromRaw(IO.readFully(archive));
+
+			try (InputStream fi = Files.newInputStream(archive.toPath());
+					InputStream bi = new BufferedInputStream(fi);
+					ArchiveInputStream o = new TarArchiveInputStream(bi)) {
+				assertEntries(o);
+			}
+
+			Thread.sleep(WAIT);
+			archive(git, archive, fmt);
+			assertEquals(UNEXPECTED_DIFFERENT_HASH, hash1,
+					ObjectId.fromRaw(IO.readFully(archive)));
+		}
+	}
+
+	@Test
+	public void archiveHeadAllFilesTgzTimestamps() throws Exception {
+		try (Git git = new Git(db)) {
+			createTestContent(git);
+			String fmt = "tgz";
+			File archive = new File(getTemporaryDirectory(),
+					"archive." + fmt);
+			archive(git, archive, fmt);
+			ObjectId hash1 = ObjectId.fromRaw(IO.readFully(archive));
+
+			try (InputStream fi = Files.newInputStream(archive.toPath());
+					InputStream bi = new BufferedInputStream(fi);
+					InputStream gzi = new GzipCompressorInputStream(bi);
+					ArchiveInputStream o = new TarArchiveInputStream(gzi)) {
+				assertEntries(o);
+			}
+
+			Thread.sleep(WAIT);
+			archive(git, archive, fmt);
+			assertEquals(UNEXPECTED_DIFFERENT_HASH, hash1,
+					ObjectId.fromRaw(IO.readFully(archive)));
+		}
+	}
+
+	@Test
+	public void archiveHeadAllFilesTbz2Timestamps() throws Exception {
+		try (Git git = new Git(db)) {
+			createTestContent(git);
+			String fmt = "tbz2";
+			File archive = new File(getTemporaryDirectory(),
+					"archive." + fmt);
+			archive(git, archive, fmt);
+			ObjectId hash1 = ObjectId.fromRaw(IO.readFully(archive));
+
+			try (InputStream fi = Files.newInputStream(archive.toPath());
+					InputStream bi = new BufferedInputStream(fi);
+					InputStream gzi = new BZip2CompressorInputStream(bi);
+					ArchiveInputStream o = new TarArchiveInputStream(gzi)) {
+				assertEntries(o);
+			}
+
+			Thread.sleep(WAIT);
+			archive(git, archive, fmt);
+			assertEquals(UNEXPECTED_DIFFERENT_HASH, hash1,
+					ObjectId.fromRaw(IO.readFully(archive)));
+		}
+	}
+
+	@Test
+	public void archiveHeadAllFilesTxzTimestamps() throws Exception {
+		try (Git git = new Git(db)) {
+			createTestContent(git);
+			String fmt = "txz";
+			File archive = new File(getTemporaryDirectory(), "archive." + fmt);
+			archive(git, archive, fmt);
+			ObjectId hash1 = ObjectId.fromRaw(IO.readFully(archive));
+
+			try (InputStream fi = Files.newInputStream(archive.toPath());
+					InputStream bi = new BufferedInputStream(fi);
+					InputStream gzi = new XZCompressorInputStream(bi);
+					ArchiveInputStream o = new TarArchiveInputStream(gzi)) {
+				assertEntries(o);
+			}
+
+			Thread.sleep(WAIT);
+			archive(git, archive, fmt);
+			assertEquals(UNEXPECTED_DIFFERENT_HASH, hash1,
+					ObjectId.fromRaw(IO.readFully(archive)));
+		}
+	}
+
+	@Test
+	public void archiveHeadAllFilesZipTimestamps() throws Exception {
+		try (Git git = new Git(db)) {
+			createTestContent(git);
+			String fmt = "zip";
+			File archive = new File(getTemporaryDirectory(), "archive." + fmt);
+			archive(git, archive, fmt);
+			ObjectId hash1 = ObjectId.fromRaw(IO.readFully(archive));
+
+			try (InputStream fi = Files.newInputStream(archive.toPath());
+					InputStream bi = new BufferedInputStream(fi);
+					ArchiveInputStream o = new ZipArchiveInputStream(bi)) {
+				assertEntries(o);
+			}
+
+			Thread.sleep(WAIT);
+			archive(git, archive, fmt);
+			assertEquals(UNEXPECTED_DIFFERENT_HASH, hash1,
+					ObjectId.fromRaw(IO.readFully(archive)));
+		}
+	}
+
+	private void createTestContent(Git git) throws IOException, GitAPIException,
+			NoFilepatternException, NoHeadException, NoMessageException,
+			UnmergedPathsException, ConcurrentRefUpdateException,
+			WrongRepositoryStateException, AbortedByHookException {
+		writeTrashFile("file_1.txt", "content_1_1");
+		git.add().addFilepattern("file_1.txt").call();
+		git.commit().setMessage("create file").call();
+
+		writeTrashFile("file_1.txt", "content_1_2");
+		writeTrashFile("file_2.txt", "content_2_2");
+		git.add().addFilepattern(".").call();
+		git.commit().setMessage("updated file").call();
+	}
+
+	private static void archive(Git git, File archive, String fmt)
+			throws GitAPIException,
+			FileNotFoundException, AmbiguousObjectException,
+			IncorrectObjectTypeException, IOException {
+		git.archive().setOutputStream(new FileOutputStream(archive))
+				.setFormat(fmt)
+				.setTree(git.getRepository().resolve("HEAD")).call();
+	}
+
+	private static void assertEntries(ArchiveInputStream o) throws IOException {
+		ArchiveEntry e;
+		int n = 0;
+		while ((e = o.getNextEntry()) != null) {
+			n++;
+			assertEquals(UNEXPECTED_LAST_MODIFIED,
+					(1250379778668L / 1000L) * 1000L,
+					e.getLastModifiedDate().getTime());
+		}
+		assertEquals(UNEXPECTED_ARCHIVE_SIZE, 2, n);
+	}
+
 	private static class MockFormat
 			implements ArchiveCommand.Format<MockOutputStream> {
 

org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CheckoutCommandTest.java

@@ -43,6 +43,7 @@
  */
 package org.eclipse.jgit.api;
 
+import static java.time.Instant.EPOCH;
 import static org.eclipse.jgit.lib.Constants.MASTER;
 import static org.eclipse.jgit.lib.Constants.R_HEADS;
 import static org.hamcrest.CoreMatchers.is;
@@ -60,6 +61,9 @@ import java.io.FileInputStream;
 import java.io.IOException;
 import java.net.MalformedURLException;
 import java.net.URISyntaxException;
+import java.nio.file.Files;
+import java.nio.file.attribute.FileTime;
+import java.time.Instant;
 
 import org.eclipse.jgit.api.CheckoutResult.Status;
 import org.eclipse.jgit.api.CreateBranchCommand.SetupUpstreamMode;
@@ -75,6 +79,7 @@ import org.eclipse.jgit.dircache.DirCache;
 import org.eclipse.jgit.dircache.DirCacheEntry;
 import org.eclipse.jgit.junit.JGitTestUtil;
 import org.eclipse.jgit.junit.RepositoryTestCase;
+import org.eclipse.jgit.junit.time.TimeUtil;
 import org.eclipse.jgit.lfs.BuiltinLFS;
 import org.eclipse.jgit.lib.ConfigConstants;
 import org.eclipse.jgit.lib.Constants;
@@ -87,6 +92,7 @@ import org.eclipse.jgit.revwalk.RevCommit;
 import org.eclipse.jgit.storage.file.FileBasedConfig;
 import org.eclipse.jgit.transport.RemoteConfig;
 import org.eclipse.jgit.transport.URIish;
+import org.eclipse.jgit.util.FS;
 import org.eclipse.jgit.util.FileUtils;
 import org.eclipse.jgit.util.SystemReader;
 import org.junit.Before;
@@ -376,14 +382,14 @@ public class CheckoutCommandTest extends RepositoryTestCase {
 
 		File file = new File(db.getWorkTree(), "Test.txt");
 		long size = file.length();
-		long mTime = file.lastModified() - 5000L;
-		assertTrue(file.setLastModified(mTime));
+		Instant mTime = TimeUtil.setLastModifiedWithOffset(file.toPath(),
+				-5000L);
 
 		DirCache cache = DirCache.lock(db.getIndexFile(), db.getFS());
 		DirCacheEntry entry = cache.getEntry("Test.txt");
 		assertNotNull(entry);
 		entry.setLength(0);
-		entry.setLastModified(0);
+		entry.setLastModified(EPOCH);
 		cache.write();
 		assertTrue(cache.commit());
 
@@ -391,10 +397,12 @@ public class CheckoutCommandTest extends RepositoryTestCase {
 		entry = cache.getEntry("Test.txt");
 		assertNotNull(entry);
 		assertEquals(0, entry.getLength());
-		assertEquals(0, entry.getLastModified());
+		assertEquals(EPOCH, entry.getLastModifiedInstant());
 
-		db.getIndexFile().setLastModified(
-				db.getIndexFile().lastModified() - 5000);
+		Files.setLastModifiedTime(db.getIndexFile().toPath(),
+				FileTime.from(FS.DETECTED
+						.lastModifiedInstant(db.getIndexFile())
+						.minusMillis(5000L)));
 
 		assertNotNull(git.checkout().setName("test").call());
 
@@ -402,7 +410,7 @@ public class CheckoutCommandTest extends RepositoryTestCase {
 		entry = cache.getEntry("Test.txt");
 		assertNotNull(entry);
 		assertEquals(size, entry.getLength());
-		assertEquals(mTime, entry.getLastModified());
+		assertEquals(mTime, entry.getLastModifiedInstant());
 	}
 
 	@Test

org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CommitCommandTest.java

@@ -65,6 +65,7 @@ import org.eclipse.jgit.dircache.DirCache;
 import org.eclipse.jgit.dircache.DirCacheBuilder;
 import org.eclipse.jgit.dircache.DirCacheEntry;
 import org.eclipse.jgit.junit.RepositoryTestCase;
+import org.eclipse.jgit.junit.time.TimeUtil;
 import org.eclipse.jgit.lib.CommitBuilder;
 import org.eclipse.jgit.lib.ConfigConstants;
 import org.eclipse.jgit.lib.Constants;
@@ -319,11 +320,11 @@ public class CommitCommandTest extends RepositoryTestCase {
 	public void commitUpdatesSmudgedEntries() throws Exception {
 		try (Git git = new Git(db)) {
 			File file1 = writeTrashFile("file1.txt", "content1");
-			assertTrue(file1.setLastModified(file1.lastModified() - 5000));
+			TimeUtil.setLastModifiedWithOffset(file1.toPath(), -5000L);
 			File file2 = writeTrashFile("file2.txt", "content2");
-			assertTrue(file2.setLastModified(file2.lastModified() - 5000));
+			TimeUtil.setLastModifiedWithOffset(file2.toPath(), -5000L);
 			File file3 = writeTrashFile("file3.txt", "content3");
-			assertTrue(file3.setLastModified(file3.lastModified() - 5000));
+			TimeUtil.setLastModifiedWithOffset(file3.toPath(), -5000L);
 
 			assertNotNull(git.add().addFilepattern("file1.txt")
 					.addFilepattern("file2.txt").addFilepattern("file3.txt").call());
@@ -354,11 +355,12 @@ public class CommitCommandTest extends RepositoryTestCase {
 			assertEquals(0, cache.getEntry("file2.txt").getLength());
 			assertEquals(0, cache.getEntry("file3.txt").getLength());
 
-			long indexTime = db.getIndexFile().lastModified();
-			db.getIndexFile().setLastModified(indexTime - 5000);
+			TimeUtil.setLastModifiedWithOffset(db.getIndexFile().toPath(),
+					-5000L);
 
 			write(file1, "content4");
-			assertTrue(file1.setLastModified(file1.lastModified() + 2500));
+
+			TimeUtil.setLastModifiedWithOffset(file1.toPath(), 2500L);
 			assertNotNull(git.commit().setMessage("edit file").setOnly("file1.txt")
 					.call());
 
@@ -376,9 +378,9 @@ public class CommitCommandTest extends RepositoryTestCase {
 	public void commitIgnoresSmudgedEntryWithDifferentId() throws Exception {
 		try (Git git = new Git(db)) {
 			File file1 = writeTrashFile("file1.txt", "content1");
-			assertTrue(file1.setLastModified(file1.lastModified() - 5000));
+			TimeUtil.setLastModifiedWithOffset(file1.toPath(), -5000L);
 			File file2 = writeTrashFile("file2.txt", "content2");
-			assertTrue(file2.setLastModified(file2.lastModified() - 5000));
+			TimeUtil.setLastModifiedWithOffset(file2.toPath(), -5000L);
 
 			assertNotNull(git.add().addFilepattern("file1.txt")
 					.addFilepattern("file2.txt").call());
@@ -407,11 +409,11 @@ public class CommitCommandTest extends RepositoryTestCase {
 			assertEquals(0, cache.getEntry("file1.txt").getLength());
 			assertEquals(0, cache.getEntry("file2.txt").getLength());
 
-			long indexTime = db.getIndexFile().lastModified();
-			db.getIndexFile().setLastModified(indexTime - 5000);
+			TimeUtil.setLastModifiedWithOffset(db.getIndexFile().toPath(),
+					-5000L);
 
 			write(file1, "content5");
-			assertTrue(file1.setLastModified(file1.lastModified() + 1000));
+			TimeUtil.setLastModifiedWithOffset(file1.toPath(), 1000L);
 
 			assertNotNull(git.commit().setMessage("edit file").setOnly("file1.txt")
 					.call());

org.eclipse.jgit.test/tst/org/eclipse/jgit/api/DiffCommandTest.java

@@ -44,7 +44,6 @@ package org.eclipse.jgit.api;
 
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
 
 import java.io.ByteArrayOutputStream;
 import java.io.File;
@@ -55,6 +54,7 @@ import java.util.List;
 import org.eclipse.jgit.diff.DiffEntry;
 import org.eclipse.jgit.diff.DiffEntry.ChangeType;
 import org.eclipse.jgit.junit.RepositoryTestCase;
+import org.eclipse.jgit.junit.time.TimeUtil;
 import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.lib.ObjectReader;
 import org.eclipse.jgit.revwalk.RevWalk;
@@ -230,7 +230,7 @@ public class DiffCommandTest extends RepositoryTestCase {
 	@Test
 	public void testNoOutputStreamSet() throws Exception {
 		File file = writeTrashFile("test.txt", "a");
-		assertTrue(file.setLastModified(file.lastModified() - 5000));
+		TimeUtil.setLastModifiedWithOffset(file.toPath(), -5000L);
 		try (Git git = new Git(db)) {
 			git.add().addFilepattern(".").call();
 			write(file, "b");

org.eclipse.jgit.test/tst/org/eclipse/jgit/api/ResetCommandTest.java

@@ -42,6 +42,7 @@
  */
 package org.eclipse.jgit.api;
 
+import static java.time.Instant.EPOCH;
 import static org.eclipse.jgit.api.ResetCommand.ResetType.HARD;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertFalse;
@@ -52,6 +53,9 @@ import static org.junit.Assert.fail;
 
 import java.io.File;
 import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.attribute.FileTime;
+import java.time.Instant;
 
 import org.eclipse.jgit.api.ResetCommand.ResetType;
 import org.eclipse.jgit.api.errors.GitAPIException;
@@ -288,13 +292,13 @@ public class ResetCommandTest extends RepositoryTestCase {
 	public void testMixedResetRetainsSizeAndModifiedTime() throws Exception {
 		git = new Git(db);
 
-		writeTrashFile("a.txt", "a").setLastModified(
-				System.currentTimeMillis() - 60 * 1000);
+		Files.setLastModifiedTime(writeTrashFile("a.txt", "a").toPath(),
+				FileTime.from(Instant.now().minusSeconds(60)));
 		assertNotNull(git.add().addFilepattern("a.txt").call());
 		assertNotNull(git.commit().setMessage("a commit").call());
 
-		writeTrashFile("b.txt", "b").setLastModified(
-				System.currentTimeMillis() - 60 * 1000);
+		Files.setLastModifiedTime(writeTrashFile("b.txt", "b").toPath(),
+				FileTime.from(Instant.now().minusSeconds(60)));
 		assertNotNull(git.add().addFilepattern("b.txt").call());
 		RevCommit commit2 = git.commit().setMessage("b commit").call();
 		assertNotNull(commit2);
@@ -304,12 +308,12 @@ public class ResetCommandTest extends RepositoryTestCase {
 		DirCacheEntry aEntry = cache.getEntry("a.txt");
 		assertNotNull(aEntry);
 		assertTrue(aEntry.getLength() > 0);
-		assertTrue(aEntry.getLastModified() > 0);
+		assertTrue(aEntry.getLastModifiedInstant().compareTo(EPOCH) > 0);
 
 		DirCacheEntry bEntry = cache.getEntry("b.txt");
 		assertNotNull(bEntry);
 		assertTrue(bEntry.getLength() > 0);
-		assertTrue(bEntry.getLastModified() > 0);
+		assertTrue(bEntry.getLastModifiedInstant().compareTo(EPOCH) > 0);
 
 		assertSameAsHead(git.reset().setMode(ResetType.MIXED)
 				.setRef(commit2.getName()).call());
@@ -318,13 +322,17 @@ public class ResetCommandTest extends RepositoryTestCase {
 
 		DirCacheEntry mixedAEntry = cache.getEntry("a.txt");
 		assertNotNull(mixedAEntry);
-		assertEquals(aEntry.getLastModified(), mixedAEntry.getLastModified());
-		assertEquals(aEntry.getLastModified(), mixedAEntry.getLastModified());
+		assertEquals(aEntry.getLastModifiedInstant(),
+				mixedAEntry.getLastModifiedInstant());
+		assertEquals(aEntry.getLastModifiedInstant(),
+				mixedAEntry.getLastModifiedInstant());
 
 		DirCacheEntry mixedBEntry = cache.getEntry("b.txt");
 		assertNotNull(mixedBEntry);
-		assertEquals(bEntry.getLastModified(), mixedBEntry.getLastModified());
-		assertEquals(bEntry.getLastModified(), mixedBEntry.getLastModified());
+		assertEquals(bEntry.getLastModifiedInstant(),
+				mixedBEntry.getLastModifiedInstant());
+		assertEquals(bEntry.getLastModifiedInstant(),
+				mixedBEntry.getLastModifiedInstant());
 	}
 
 	@Test

org.eclipse.jgit.test/tst/org/eclipse/jgit/dircache/DirCacheBuilderTest.java

@@ -53,6 +53,7 @@ import static org.junit.Assert.assertTrue;
 import static org.junit.Assert.fail;
 
 import java.io.File;
+import java.time.Instant;
 
 import org.eclipse.jgit.events.IndexChangedEvent;
 import org.eclipse.jgit.events.IndexChangedListener;
@@ -99,7 +100,7 @@ public class DirCacheBuilderTest extends RepositoryTestCase {
 	public void testBuildOneFile_FinishWriteCommit() throws Exception {
 		final String path = "a-file-path";
 		final FileMode mode = FileMode.REGULAR_FILE;
-		final long lastModified = 1218123387057L;
+		final Instant lastModified = Instant.ofEpochMilli(1218123387057L);
 		final int length = 1342;
 		final DirCacheEntry entOrig;
 		{
@@ -117,7 +118,7 @@ public class DirCacheBuilderTest extends RepositoryTestCase {
 			assertEquals(ObjectId.zeroId(), entOrig.getObjectId());
 			assertEquals(mode.getBits(), entOrig.getRawMode());
 			assertEquals(0, entOrig.getStage());
-			assertEquals(lastModified, entOrig.getLastModified());
+			assertEquals(lastModified, entOrig.getLastModifiedInstant());
 			assertEquals(length, entOrig.getLength());
 			assertFalse(entOrig.isAssumeValid());
 			b.add(entOrig);
@@ -139,7 +140,7 @@ public class DirCacheBuilderTest extends RepositoryTestCase {
 			assertEquals(ObjectId.zeroId(), entOrig.getObjectId());
 			assertEquals(mode.getBits(), entOrig.getRawMode());
 			assertEquals(0, entOrig.getStage());
-			assertEquals(lastModified, entOrig.getLastModified());
+			assertEquals(lastModified, entOrig.getLastModifiedInstant());
 			assertEquals(length, entOrig.getLength());
 			assertFalse(entOrig.isAssumeValid());
 		}
@@ -149,7 +150,7 @@ public class DirCacheBuilderTest extends RepositoryTestCase {
 	public void testBuildOneFile_Commit() throws Exception {
 		final String path = "a-file-path";
 		final FileMode mode = FileMode.REGULAR_FILE;
-		final long lastModified = 1218123387057L;
+		final Instant lastModified = Instant.ofEpochMilli(1218123387057L);
 		final int length = 1342;
 		final DirCacheEntry entOrig;
 		{
@@ -167,7 +168,7 @@ public class DirCacheBuilderTest extends RepositoryTestCase {
 			assertEquals(ObjectId.zeroId(), entOrig.getObjectId());
 			assertEquals(mode.getBits(), entOrig.getRawMode());
 			assertEquals(0, entOrig.getStage());
-			assertEquals(lastModified, entOrig.getLastModified());
+			assertEquals(lastModified, entOrig.getLastModifiedInstant());
 			assertEquals(length, entOrig.getLength());
 			assertFalse(entOrig.isAssumeValid());
 			b.add(entOrig);
@@ -187,7 +188,7 @@ public class DirCacheBuilderTest extends RepositoryTestCase {
 			assertEquals(ObjectId.zeroId(), entOrig.getObjectId());
 			assertEquals(mode.getBits(), entOrig.getRawMode());
 			assertEquals(0, entOrig.getStage());
-			assertEquals(lastModified, entOrig.getLastModified());
+			assertEquals(lastModified, entOrig.getLastModifiedInstant());
 			assertEquals(length, entOrig.getLength());
 			assertFalse(entOrig.isAssumeValid());
 		}
@@ -204,7 +205,7 @@ public class DirCacheBuilderTest extends RepositoryTestCase {
 		final String path = "a-file-path";
 		final FileMode mode = FileMode.REGULAR_FILE;
 		// "old" date in 2008
-		final long lastModified = 1218123387057L;
+		final Instant lastModified = Instant.ofEpochMilli(1218123387057L);
 		final int length = 1342;
 		DirCacheEntry entOrig;
 		boolean receivedEvent = false;

org.eclipse.jgit.test/tst/org/eclipse/jgit/dircache/DirCacheEntryTest.java

@@ -43,6 +43,7 @@
 
 package org.eclipse.jgit.dircache;
 
+import static java.time.Instant.EPOCH;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertSame;
@@ -188,7 +189,7 @@ public class DirCacheEntryTest {
 		e.setAssumeValid(false);
 		e.setCreationTime(2L);
 		e.setFileMode(FileMode.EXECUTABLE_FILE);
-		e.setLastModified(3L);
+		e.setLastModified(EPOCH.plusMillis(3L));
 		e.setLength(100L);
 		e.setObjectId(ObjectId
 				.fromString("0123456789012345678901234567890123456789"));
@@ -199,7 +200,7 @@ public class DirCacheEntryTest {
 		f.setAssumeValid(true);
 		f.setCreationTime(10L);
 		f.setFileMode(FileMode.SYMLINK);
-		f.setLastModified(20L);
+		f.setLastModified(EPOCH.plusMillis(20L));
 		f.setLength(100000000L);
 		f.setObjectId(ObjectId
 				.fromString("1234567890123456789012345678901234567890"));
@@ -212,7 +213,7 @@ public class DirCacheEntryTest {
 				ObjectId.fromString("1234567890123456789012345678901234567890"),
 				e.getObjectId());
 		assertEquals(FileMode.SYMLINK, e.getFileMode());
-		assertEquals(20L, e.getLastModified());
+		assertEquals(EPOCH.plusMillis(20L), e.getLastModifiedInstant());
 		assertEquals(100000000L, e.getLength());
 		if (keepStage)
 			assertEquals(DirCacheEntry.STAGE_2, e.getStage());

org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/dfs/DfsGarbageCollectorTest.java

@@ -976,7 +976,7 @@ public class DfsGarbageCollectorTest {
 				rw.markStart(rw.parseCommit(ref.getObjectId()));
 			}
 			for (RevCommit next; (next = rw.next()) != null;) {
-				if (AnyObjectId.equals(next, id)) {
+				if (AnyObjectId.isEqual(next, id)) {
 					return true;
 				}
 			}

org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/BatchRefUpdateTest.java

@@ -938,6 +938,7 @@ public class BatchRefUpdateTest extends LocalDiskRepositoryTestCase {
 		REJECTED_MISSING_OBJECT(ReceiveCommand.Result.REJECTED_MISSING_OBJECT),
 		TRANSACTION_ABORTED(ReceiveCommand::isTransactionAborted);
 
+		@SuppressWarnings("ImmutableEnumChecker")
 		final Predicate<? super ReceiveCommand> p;
 
 		private Result(Predicate<? super ReceiveCommand> p) {

org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/ConcurrentRepackTest.java

@@ -56,6 +56,7 @@ import java.io.File;
 import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.OutputStream;
+import java.time.Instant;
 
 import org.eclipse.jgit.errors.IncorrectObjectTypeException;
 import org.eclipse.jgit.errors.MissingObjectException;
@@ -71,6 +72,7 @@ import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.revwalk.RevObject;
 import org.eclipse.jgit.revwalk.RevWalk;
 import org.eclipse.jgit.storage.file.WindowCacheConfig;
+import org.eclipse.jgit.util.FS;
 import org.eclipse.jgit.util.FileUtils;
 import org.junit.After;
 import org.junit.Before;
@@ -235,7 +237,8 @@ public class ConcurrentRepackTest extends RepositoryTestCase {
 
 	private static void write(File[] files, PackWriter pw)
 			throws IOException {
-		final long begin = files[0].getParentFile().lastModified();
+		final Instant begin = FS.DETECTED
+				.lastModifiedInstant(files[0].getParentFile());
 		NullProgressMonitor m = NullProgressMonitor.INSTANCE;
 
 		try (OutputStream out = new BufferedOutputStream(
@@ -252,7 +255,8 @@ public class ConcurrentRepackTest extends RepositoryTestCase {
 	}
 
 	private static void delete(File[] list) throws IOException {
-		final long begin = list[0].getParentFile().lastModified();
+		final Instant begin = FS.DETECTED
+				.lastModifiedInstant(list[0].getParentFile());
 		for (File f : list) {
 			FileUtils.delete(f);
 			assertFalse(f + " was removed", f.exists());
@@ -260,14 +264,14 @@ public class ConcurrentRepackTest extends RepositoryTestCase {
 		touch(begin, list[0].getParentFile());
 	}
 
-	private static void touch(long begin, File dir) {
-		while (begin >= dir.lastModified()) {
+	private static void touch(Instant begin, File dir) throws IOException {
+		while (begin.compareTo(FS.DETECTED.lastModifiedInstant(dir)) >= 0) {
 			try {
 				Thread.sleep(25);
 			} catch (InterruptedException ie) {
 				//
 			}
-			dir.setLastModified(System.currentTimeMillis());
+			FS.DETECTED.setLastModified(dir.toPath(), Instant.now());
 		}
 	}
 

org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/FileSnapshotTest.java

@@ -42,49 +42,68 @@
  */
 package org.eclipse.jgit.internal.storage.file;
 
+import static org.eclipse.jgit.junit.JGitTestUtil.read;
+import static org.eclipse.jgit.junit.JGitTestUtil.write;
+import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertFalse;
 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.nio.file.Files;
+import java.nio.file.Path;
 import java.nio.file.StandardCopyOption;
+import java.nio.file.StandardOpenOption;
 import java.nio.file.attribute.FileTime;
+import java.time.Duration;
+import java.time.Instant;
 import java.util.ArrayList;
-import java.util.List;
+import java.util.concurrent.TimeUnit;
 
+import org.eclipse.jgit.util.FS;
+import org.eclipse.jgit.util.FS.FileStoreAttributes;
 import org.eclipse.jgit.util.FileUtils;
+import org.eclipse.jgit.util.Stats;
 import org.eclipse.jgit.util.SystemReader;
 import org.junit.After;
 import org.junit.Assume;
 import org.junit.Before;
 import org.junit.Test;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 public class FileSnapshotTest {
+	private static final Logger LOG = LoggerFactory
+			.getLogger(FileSnapshotTest.class);
 
-	private List<File> files = new ArrayList<>();
+	private Path trash;
 
-	private File trash;
+	private FileStoreAttributes fsAttrCache;
 
 	@Before
 	public void setUp() throws Exception {
-		trash = File.createTempFile("tmp_", "");
-		trash.delete();
-		assertTrue("mkdir " + trash, trash.mkdir());
+		trash = Files.createTempDirectory("tmp_");
+		// measure timer resolution before the test to avoid time critical tests
+		// are affected by time needed for measurement
+		fsAttrCache = FS
+				.getFileStoreAttributes(trash.getParent());
 	}
 
 	@Before
 	@After
 	public void tearDown() throws Exception {
-		FileUtils.delete(trash, FileUtils.RECURSIVE | FileUtils.SKIP_MISSING);
+		FileUtils.delete(trash.toFile(),
+				FileUtils.RECURSIVE | FileUtils.SKIP_MISSING);
 	}
 
-	private static void waitNextSec(File f) {
-		long initialLastModified = f.lastModified();
+	private static void waitNextTick(Path f) throws IOException {
+		Instant initialLastModified = FS.DETECTED.lastModifiedInstant(f);
 		do {
-			f.setLastModified(System.currentTimeMillis());
-		} while (f.lastModified() == initialLastModified);
+			FS.DETECTED.setLastModified(f, Instant.now());
+		} while (FS.DETECTED.lastModifiedInstant(f)
+				.equals(initialLastModified));
 	}
 
 	/**
@@ -94,12 +113,12 @@ public class FileSnapshotTest {
 	 */
 	@Test
 	public void testActuallyIsModifiedTrivial() throws Exception {
-		File f1 = createFile("simple");
-		waitNextSec(f1);
-		FileSnapshot save = FileSnapshot.save(f1);
+		Path f1 = createFile("simple");
+		waitNextTick(f1);
+		FileSnapshot save = FileSnapshot.save(f1.toFile());
 		append(f1, (byte) 'x');
-		waitNextSec(f1);
-		assertTrue(save.isModified(f1));
+		waitNextTick(f1);
+		assertTrue(save.isModified(f1.toFile()));
 	}
 
 	/**
@@ -112,11 +131,17 @@ public class FileSnapshotTest {
 	 */
 	@Test
 	public void testNewFileWithWait() throws Exception {
-		File f1 = createFile("newfile");
-		waitNextSec(f1);
-		FileSnapshot save = FileSnapshot.save(f1);
-		Thread.sleep(1500);
-		assertTrue(save.isModified(f1));
+		// if filesystem timestamp resolution is high the snapshot won't be
+		// racily clean
+		Assume.assumeTrue(
+				fsAttrCache.getFsTimestampResolution()
+						.compareTo(Duration.ofMillis(10)) > 0);
+		Path f1 = createFile("newfile");
+		waitNextTick(f1);
+		FileSnapshot save = FileSnapshot.save(f1.toFile());
+		TimeUnit.NANOSECONDS.sleep(
+				fsAttrCache.getFsTimestampResolution().dividedBy(2).toNanos());
+		assertTrue(save.isModified(f1.toFile()));
 	}
 
 	/**
@@ -126,9 +151,33 @@ public class FileSnapshotTest {
 	 */
 	@Test
 	public void testNewFileNoWait() throws Exception {
-		File f1 = createFile("newfile");
-		FileSnapshot save = FileSnapshot.save(f1);
-		assertTrue(save.isModified(f1));
+		// if filesystem timestamp resolution is smaller than time needed to
+		// create a file and FileSnapshot the snapshot won't be racily clean
+		Assume.assumeTrue(fsAttrCache.getFsTimestampResolution()
+				.compareTo(Duration.ofMillis(10)) > 0);
+		for (int i = 0; i < 50; i++) {
+			Instant start = Instant.now();
+			Path f1 = createFile("newfile");
+			FileSnapshot save = FileSnapshot.save(f1.toFile());
+			Duration res = FS.getFileStoreAttributes(f1)
+					.getFsTimestampResolution();
+			Instant end = Instant.now();
+			if (Duration.between(start, end)
+					.compareTo(res.multipliedBy(2)) > 0) {
+				// This test is racy: under load, there may be a delay between createFile() and
+				// FileSnapshot.save(). This can stretch the time between the read TS and FS
+				// creation TS to the point that it exceeds the FS granularity, and we
+				// conclude it cannot be racily clean, and therefore must be really clean.
+				//
+				// This should be relatively uncommon.
+				continue;
+			}
+			// The file wasn't really modified, but it looks just like a "maybe racily clean"
+			// file.
+			assertTrue(save.isModified(f1.toFile()));
+			return;
+		}
+		fail("too much load for this test");
 	}
 
 	/**
@@ -142,19 +191,19 @@ public class FileSnapshotTest {
 	@Test
 	public void testSimulatePackfileReplacement() throws Exception {
 		Assume.assumeFalse(SystemReader.getInstance().isWindows());
-		File f1 = createFile("file"); // inode y
-		File f2 = createFile("fool"); // Guarantees new inode x
+		Path f1 = createFile("file"); // inode y
+		Path f2 = createFile("fool"); // Guarantees new inode x
 		// wait on f2 since this method resets lastModified of the file
 		// and leaves lastModified of f1 untouched
-		waitNextSec(f2);
-		waitNextSec(f2);
-		FileTime timestamp = Files.getLastModifiedTime(f1.toPath());
-		FileSnapshot save = FileSnapshot.save(f1);
-		Files.move(f2.toPath(), f1.toPath(), // Now "file" is inode x
+		waitNextTick(f2);
+		waitNextTick(f2);
+		FileTime timestamp = Files.getLastModifiedTime(f1);
+		FileSnapshot save = FileSnapshot.save(f1.toFile());
+		Files.move(f2, f1, // Now "file" is inode x
 				StandardCopyOption.REPLACE_EXISTING,
 				StandardCopyOption.ATOMIC_MOVE);
-		Files.setLastModifiedTime(f1.toPath(), timestamp);
-		assertTrue(save.isModified(f1));
+		Files.setLastModifiedTime(f1, timestamp);
+		assertTrue(save.isModified(f1.toFile()));
 		assertTrue("unexpected change of fileKey", save.wasFileKeyChanged());
 		assertFalse("unexpected size change", save.wasSizeChanged());
 		assertFalse("unexpected lastModified change",
@@ -171,24 +220,83 @@ public class FileSnapshotTest {
 	 */
 	@Test
 	public void testFileSizeChanged() throws Exception {
-		File f = createFile("file");
-		FileTime timestamp = Files.getLastModifiedTime(f.toPath());
-		FileSnapshot save = FileSnapshot.save(f);
+		Path f = createFile("file");
+		FileTime timestamp = Files.getLastModifiedTime(f);
+		FileSnapshot save = FileSnapshot.save(f.toFile());
 		append(f, (byte) 'x');
-		Files.setLastModifiedTime(f.toPath(), timestamp);
-		assertTrue(save.isModified(f));
+		Files.setLastModifiedTime(f, timestamp);
+		assertTrue(save.isModified(f.toFile()));
 		assertTrue(save.wasSizeChanged());
 	}
 
-	private File createFile(String string) throws IOException {
-		trash.mkdirs();
-		File f = File.createTempFile(string, "tdat", trash);
-		files.add(f);
-		return f;
+	@Test
+	public void fileSnapshotEquals() throws Exception {
+		// 0 sized FileSnapshot.
+		FileSnapshot fs1 = FileSnapshot.MISSING_FILE;
+		// UNKNOWN_SIZE FileSnapshot.
+		FileSnapshot fs2 = FileSnapshot.save(fs1.lastModifiedInstant());
+
+		assertTrue(fs1.equals(fs2));
+		assertTrue(fs2.equals(fs1));
+	}
+
+	@SuppressWarnings("boxing")
+	@Test
+	public void detectFileModified() throws IOException {
+		int failures = 0;
+		long racyNanos = 0;
+		final int COUNT = 10000;
+		ArrayList<Long> deltas = new ArrayList<>();
+		File f = createFile("test").toFile();
+		for (int i = 0; i < COUNT; i++) {
+			write(f, "a");
+			FileSnapshot snapshot = FileSnapshot.save(f);
+			assertEquals("file should contain 'a'", "a", read(f));
+			write(f, "b");
+			if (!snapshot.isModified(f)) {
+				deltas.add(snapshot.lastDelta());
+				racyNanos = snapshot.lastRacyThreshold();
+				failures++;
+			}
+			assertEquals("file should contain 'b'", "b", read(f));
+		}
+		if (failures > 0) {
+			Stats stats = new Stats();
+			LOG.debug(
+					"delta [ns] since modification FileSnapshot failed to detect");
+			for (Long d : deltas) {
+				stats.add(d);
+				LOG.debug(String.format("%,d", d));
+			}
+			LOG.error(
+					"count, failures, eff. racy threshold [ns], delta min [ns],"
+							+ " delta max [ns], delta avg [ns],"
+							+ " delta stddev [ns]");
+			LOG.error(String.format(
+					"%,d, %,d, %,d, %,.0f, %,.0f, %,.0f, %,.0f", COUNT,
+					failures, racyNanos, stats.min(), stats.max(),
+					stats.avg(), stats.stddev()));
+		}
+		assertTrue(
+				String.format(
+						"FileSnapshot: failures to detect file modifications"
+								+ " %d out of %d\n"
+								+ "timestamp resolution %d µs"
+								+ " min racy threshold %d µs"
+						, failures, COUNT,
+						fsAttrCache.getFsTimestampResolution().toNanos() / 1000,
+						fsAttrCache.getMinimalRacyInterval().toNanos() / 1000),
+				failures == 0);
+	}
+
+	private Path createFile(String string) throws IOException {
+		Files.createDirectories(trash);
+		return Files.createTempFile(trash, string, "tdat");
 	}
 
-	private static void append(File f, byte b) throws IOException {
-		try (FileOutputStream os = new FileOutputStream(f, true)) {
+	private static void append(Path f, byte b) throws IOException {
+		try (OutputStream os = Files.newOutputStream(f,
+				StandardOpenOption.APPEND)) {
 			os.write(b);
 		}
 	}

org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/GcTestCase.java

@@ -147,9 +147,10 @@ public abstract class GcTestCase extends LocalDiskRepositoryTestCase {
 		return tip;
 	}
 
-	protected long lastModified(AnyObjectId objectId) throws IOException {
-		return repo.getFS().lastModified(
-				repo.getObjectDatabase().fileFor(objectId));
+	protected long lastModified(AnyObjectId objectId) {
+		return repo.getFS()
+				.lastModifiedInstant(repo.getObjectDatabase().fileFor(objectId))
+				.toEpochMilli();
 	}
 
 	protected static void fsTick() throws InterruptedException, IOException {

org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/ObjectDirectoryTest.java

@@ -65,6 +65,7 @@ import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.revwalk.RevCommit;
 import org.eclipse.jgit.storage.file.FileBasedConfig;
+import org.eclipse.jgit.util.FS;
 import org.junit.Assume;
 import org.junit.Rule;
 import org.junit.Test;
@@ -157,19 +158,22 @@ public class ObjectDirectoryTest extends RepositoryTestCase {
 
 			// To deal with racy-git situations JGit's Filesnapshot class will
 			// report a file/folder potentially dirty if
-			// cachedLastReadTime-cachedLastModificationTime < 2500ms. This
-			// causes JGit to always rescan a file after modification. But:
-			// this was true only if the difference between current system time
-			// and cachedLastModification time was less than 2500ms. If the
-			// modification is more than 2500ms ago we may have reported a
-			// file/folder to be clean although it has not been rescanned. A
-			// Bug. To show the bug we sleep for more than 2500ms
+			// cachedLastReadTime-cachedLastModificationTime < filesystem
+			// timestamp resolution. This causes JGit to always rescan a file
+			// after modification. But: this was true only if the difference
+			// between current system time and cachedLastModification time was
+			// less than 2500ms. If the modification is more than 2500ms ago we
+			// may have reported a file/folder to be clean although it has not
+			// been rescanned. A bug. To show the bug we sleep for more than
+			// 2500ms
 			Thread.sleep(2600);
 
 			File[] ret = packsFolder.listFiles(
 					(File dir, String name) -> name.endsWith(".pack"));
 			assertTrue(ret != null && ret.length == 1);
-			Assume.assumeTrue(tmpFile.lastModified() == ret[0].lastModified());
+			FS fs = db.getFS();
+			Assume.assumeTrue(fs.lastModifiedInstant(tmpFile)
+					.equals(fs.lastModifiedInstant(ret[0])));
 
 			// all objects are in a new packfile but we will not detect it
 			assertFalse(receivingDB.getObjectDatabase().has(unknownID));

org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/PackFileSnapshotTest.java

@@ -59,6 +59,7 @@ import java.nio.file.StandardCopyOption;
 import java.nio.file.StandardOpenOption;
 //import java.nio.file.attribute.BasicFileAttributes;
 import java.text.ParseException;
+import java.time.Instant;
 import java.util.Collection;
 import java.util.Iterator;
 import java.util.Random;
@@ -80,6 +81,7 @@ import org.eclipse.jgit.lib.ConfigConstants;
 import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.storage.file.FileBasedConfig;
 import org.eclipse.jgit.storage.pack.PackConfig;
+import org.eclipse.jgit.util.FS;
 import org.junit.Test;
 
 public class PackFileSnapshotTest extends RepositoryTestCase {
@@ -188,7 +190,8 @@ public class PackFileSnapshotTest extends RepositoryTestCase {
 		AnyObjectId chk1 = pf.getPackChecksum();
 		String name = pf.getPackName();
 		Long length = Long.valueOf(pf.getPackFile().length());
-		long m1 = packFilePath.toFile().lastModified();
+		FS fs = db.getFS();
+		Instant m1 = fs.lastModifiedInstant(packFilePath);
 
 		// Wait for a filesystem timer tick to enhance probability the rest of
 		// this test is done before the filesystem timer ticks again.
@@ -198,15 +201,15 @@ public class PackFileSnapshotTest extends RepositoryTestCase {
 		// content and checksum are different since compression level differs
 		AnyObjectId chk2 = repackAndCheck(6, name, length, chk1)
 				.getPackChecksum();
-		long m2 = packFilePath.toFile().lastModified();
-		assumeFalse(m2 == m1);
+		Instant m2 = fs.lastModifiedInstant(packFilePath);
+		assumeFalse(m2.equals(m1));
 
 		// Repack to create packfile with same name, length. Lastmodified is
 		// equal to the previous one because we are in the same filesystem timer
 		// slot. Content and its checksum are different
 		AnyObjectId chk3 = repackAndCheck(7, name, length, chk2)
 				.getPackChecksum();
-		long m3 = packFilePath.toFile().lastModified();
+		Instant m3 = fs.lastModifiedInstant(packFilePath);
 
 		// ask for an unknown git object to force jgit to rescan the list of
 		// available packs. If we would ask for a known objectid then JGit would
@@ -214,7 +217,7 @@ public class PackFileSnapshotTest extends RepositoryTestCase {
 		db.getObjectDatabase().has(unknownID);
 		assertEquals(chk3, getSinglePack(db.getObjectDatabase().getPacks())
 				.getPackChecksum());
-		assumeTrue(m3 == m2);
+		assumeTrue(m3.equals(m2));
 	}
 
 	// Try repacking so fast that we get two new packs which differ only in
@@ -253,7 +256,8 @@ public class PackFileSnapshotTest extends RepositoryTestCase {
 		// Repack to create third packfile
 		AnyObjectId chk3 = repackAndCheck(7, name, length, chk2)
 				.getPackChecksum();
-		long m3 = packFilePath.toFile().lastModified();
+		FS fs = db.getFS();
+		Instant m3 = fs.lastModifiedInstant(packFilePath);
 		db.getObjectDatabase().has(unknownID);
 		assertEquals(chk3, getSinglePack(db.getObjectDatabase().getPacks())
 				.getPackChecksum());
@@ -265,8 +269,8 @@ public class PackFileSnapshotTest extends RepositoryTestCase {
 		// Copy copy2 to packfile data to force modification of packfile without
 		// changing the packfile's filekey.
 		copyPack(packFileBasePath, ".copy2", "");
-		long m2 = packFilePath.toFile().lastModified();
-		assumeFalse(m3 == m2);
+		Instant m2 = fs.lastModifiedInstant(packFilePath);
+		assumeFalse(m3.equals(m2));
 
 		db.getObjectDatabase().has(unknownID);
 		assertEquals(chk2, getSinglePack(db.getObjectDatabase().getPacks())
@@ -275,8 +279,8 @@ public class PackFileSnapshotTest extends RepositoryTestCase {
 		// Copy copy2 to packfile data to force modification of packfile without
 		// changing the packfile's filekey.
 		copyPack(packFileBasePath, ".copy1", "");
-		long m1 = packFilePath.toFile().lastModified();
-		assumeTrue(m2 == m1);
+		Instant m1 = fs.lastModifiedInstant(packFilePath);
+		assumeTrue(m2.equals(m1));
 		db.getObjectDatabase().has(unknownID);
 		assertEquals(chk1, getSinglePack(db.getObjectDatabase().getPacks())
 				.getPackChecksum());

org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/RefDirectoryTest.java

@@ -60,6 +60,7 @@ import static org.junit.Assert.fail;
 
 import java.io.File;
 import java.io.IOException;
+import java.time.Instant;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
@@ -71,6 +72,7 @@ import org.eclipse.jgit.errors.LockFailedException;
 import org.eclipse.jgit.events.ListenerHandle;
 import org.eclipse.jgit.events.RefsChangedEvent;
 import org.eclipse.jgit.junit.LocalDiskRepositoryTestCase;
+import org.eclipse.jgit.junit.Repeat;
 import org.eclipse.jgit.junit.TestRepository;
 import org.eclipse.jgit.lib.AnyObjectId;
 import org.eclipse.jgit.lib.Ref;
@@ -79,6 +81,7 @@ import org.eclipse.jgit.lib.RefDatabase;
 import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.revwalk.RevCommit;
 import org.eclipse.jgit.revwalk.RevTag;
+import org.eclipse.jgit.util.FS;
 import org.junit.Before;
 import org.junit.Test;
 
@@ -666,6 +669,7 @@ public class RefDirectoryTest extends LocalDiskRepositoryTestCase {
 		assertEquals(B, all.get(HEAD).getObjectId());
 	}
 
+	@Repeat(n = 100, abortOnFailure = false)
 	@Test
 	public void testFindRef_DiscoversModifiedLoose() throws IOException {
 		Map<String, Ref> all;
@@ -1361,10 +1365,8 @@ public class RefDirectoryTest extends LocalDiskRepositoryTestCase {
 	private void writePackedRefs(String content) throws IOException {
 		File pr = new File(diskRepo.getDirectory(), "packed-refs");
 		write(pr, content);
-
-		final long now = System.currentTimeMillis();
-		final int oneHourAgo = 3600 * 1000;
-		pr.setLastModified(now - oneHourAgo);
+		FS fs = diskRepo.getFS();
+		fs.setLastModified(pr.toPath(), Instant.now().minusSeconds(3600));
 	}
 
 	private void deleteLooseRef(String name) {

org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/T0003_BasicTest.java

@@ -59,6 +59,7 @@ import java.io.File;
 import java.io.FileInputStream;
 import java.io.IOException;
 import java.io.UnsupportedEncodingException;
+import java.time.Instant;
 
 import org.eclipse.jgit.errors.ConfigInvalidException;
 import org.eclipse.jgit.errors.IncorrectObjectTypeException;
@@ -82,6 +83,7 @@ import org.eclipse.jgit.revwalk.RevWalk;
 import org.eclipse.jgit.storage.file.FileBasedConfig;
 import org.eclipse.jgit.storage.file.FileRepositoryBuilder;
 import org.eclipse.jgit.test.resources.SampleDataRepositoryTestCase;
+import org.eclipse.jgit.util.FS;
 import org.eclipse.jgit.util.FileUtils;
 import org.eclipse.jgit.util.IO;
 import org.junit.Rule;
@@ -790,12 +792,14 @@ public class T0003_BasicTest extends SampleDataRepositoryTestCase {
 	 *
 	 * @param name
 	 *            the file in the repository to force a time change on.
+	 * @throws IOException
 	 */
-	private void BUG_WorkAroundRacyGitIssues(String name) {
+	private void BUG_WorkAroundRacyGitIssues(String name) throws IOException {
 		File path = new File(db.getDirectory(), name);
-		long old = path.lastModified();
+		FS fs = db.getFS();
+		Instant old = fs.lastModifiedInstant(path);
 		long set = 1250379778668L; // Sat Aug 15 20:12:58 GMT-03:30 2009
-		path.setLastModified(set);
-		assertTrue("time changed", old != path.lastModified());
+		fs.setLastModified(path.toPath(), Instant.ofEpochMilli(set));
+		assertFalse("time changed", old.equals(fs.lastModifiedInstant(path)));
 	}
 }

org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/ConfigTest.java

@@ -51,8 +51,10 @@ package org.eclipse.jgit.lib;
 import static java.nio.charset.StandardCharsets.UTF_8;
 import static java.util.concurrent.TimeUnit.DAYS;
 import static java.util.concurrent.TimeUnit.HOURS;
+import static java.util.concurrent.TimeUnit.MICROSECONDS;
 import static java.util.concurrent.TimeUnit.MILLISECONDS;
 import static java.util.concurrent.TimeUnit.MINUTES;
+import static java.util.concurrent.TimeUnit.NANOSECONDS;
 import static java.util.concurrent.TimeUnit.SECONDS;
 import static org.eclipse.jgit.util.FileUtils.pathToString;
 import static org.junit.Assert.assertArrayEquals;
@@ -1224,8 +1226,18 @@ public class ConfigTest {
 
 	@Test
 	public void testTimeUnit() throws ConfigInvalidException {
+		assertEquals(0, parseTime("0", NANOSECONDS));
+		assertEquals(2, parseTime("2ns", NANOSECONDS));
+		assertEquals(200, parseTime("200 nanoseconds", NANOSECONDS));
+
+		assertEquals(0, parseTime("0", MICROSECONDS));
+		assertEquals(2, parseTime("2us", MICROSECONDS));
+		assertEquals(2, parseTime("2000 nanoseconds", MICROSECONDS));
+		assertEquals(200, parseTime("200 microseconds", MICROSECONDS));
+
 		assertEquals(0, parseTime("0", MILLISECONDS));
 		assertEquals(2, parseTime("2ms", MILLISECONDS));
+		assertEquals(2, parseTime("2000microseconds", MILLISECONDS));
 		assertEquals(200, parseTime("200 milliseconds", MILLISECONDS));
 
 		assertEquals(0, parseTime("0s", SECONDS));

org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/IndexModificationTimesTest.java

@@ -37,8 +37,12 @@
  */
 package org.eclipse.jgit.lib;
 
+import static java.time.Instant.EPOCH;
+import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertTrue;
 
+import java.time.Instant;
+
 import org.eclipse.jgit.api.Git;
 import org.eclipse.jgit.dircache.DirCache;
 import org.eclipse.jgit.dircache.DirCacheEntry;
@@ -63,11 +67,11 @@ public class IndexModificationTimesTest extends RepositoryTestCase {
 			DirCacheEntry entry = dc.getEntry(path);
 			DirCacheEntry entry2 = dc.getEntry(path);
 
-			assertTrue("last modified shall not be zero!",
-					entry.getLastModified() != 0);
+			assertFalse("last modified shall not be the epoch!",
+					entry.getLastModifiedInstant().equals(EPOCH));
 
-			assertTrue("last modified shall not be zero!",
-					entry2.getLastModified() != 0);
+			assertFalse("last modified shall not be the epoch!",
+					entry2.getLastModifiedInstant().equals(EPOCH));
 
 			writeTrashFile(path, "new content");
 			git.add().addFilepattern(path).call();
@@ -77,11 +81,11 @@ public class IndexModificationTimesTest extends RepositoryTestCase {
 			entry = dc.getEntry(path);
 			entry2 = dc.getEntry(path);
 
-			assertTrue("last modified shall not be zero!",
-					entry.getLastModified() != 0);
+			assertFalse("last modified shall not be the epoch!",
+					entry.getLastModifiedInstant().equals(EPOCH));
 
-			assertTrue("last modified shall not be zero!",
-					entry2.getLastModified() != 0);
+			assertFalse("last modified shall not be the epoch!",
+					entry2.getLastModifiedInstant().equals(EPOCH));
 		}
 	}
 
@@ -97,7 +101,7 @@ public class IndexModificationTimesTest extends RepositoryTestCase {
 			DirCache dc = db.readDirCache();
 			DirCacheEntry entry = dc.getEntry(path);
 
-			long masterLastMod = entry.getLastModified();
+			Instant masterLastMod = entry.getLastModifiedInstant();
 
 			git.checkout().setCreateBranch(true).setName("side").call();
 
@@ -110,7 +114,7 @@ public class IndexModificationTimesTest extends RepositoryTestCase {
 			dc = db.readDirCache();
 			entry = dc.getEntry(path);
 
-			long sideLastMode = entry.getLastModified();
+			Instant sideLastMod = entry.getLastModifiedInstant();
 
 			Thread.sleep(2000);
 
@@ -120,9 +124,10 @@ public class IndexModificationTimesTest extends RepositoryTestCase {
 			dc = db.readDirCache();
 			entry = dc.getEntry(path);
 
-			assertTrue("shall have equal mod time!", masterLastMod == sideLastMode);
-			assertTrue("shall not equal master timestamp!",
-					entry.getLastModified() == masterLastMod);
+			assertTrue("shall have equal mod time!",
+					masterLastMod.equals(sideLastMod));
+			assertTrue("shall have equal master timestamp!",
+					entry.getLastModifiedInstant().equals(masterLastMod));
 		}
 	}
 

org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/RacyGitTests.java

@@ -42,88 +42,26 @@
  */
 package org.eclipse.jgit.lib;
 
-import static java.lang.Long.valueOf;
 import static java.nio.charset.StandardCharsets.UTF_8;
 import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertTrue;
 
 import java.io.File;
 import java.io.FileOutputStream;
 import java.io.IOException;
-import java.util.TreeSet;
+import java.time.Instant;
 
 import org.eclipse.jgit.api.Git;
+import org.eclipse.jgit.dircache.DirCache;
 import org.eclipse.jgit.junit.RepositoryTestCase;
+import org.eclipse.jgit.junit.time.TimeUtil;
 import org.eclipse.jgit.treewalk.FileTreeIterator;
-import org.eclipse.jgit.treewalk.FileTreeIteratorWithTimeControl;
-import org.eclipse.jgit.treewalk.NameConflictTreeWalk;
-import org.eclipse.jgit.util.FileUtils;
+import org.eclipse.jgit.treewalk.WorkingTreeOptions;
+import org.eclipse.jgit.util.FS;
 import org.junit.Test;
 
 public class RacyGitTests extends RepositoryTestCase {
-	@Test
-	public void testIterator()
-			throws IllegalStateException, IOException, InterruptedException {
-		TreeSet<Long> modTimes = new TreeSet<>();
-		File lastFile = null;
-		for (int i = 0; i < 10; i++) {
-			lastFile = new File(db.getWorkTree(), "0." + i);
-			FileUtils.createNewFile(lastFile);
-			if (i == 5)
-				fsTick(lastFile);
-		}
-		modTimes.add(valueOf(fsTick(lastFile)));
-		for (int i = 0; i < 10; i++) {
-			lastFile = new File(db.getWorkTree(), "1." + i);
-			FileUtils.createNewFile(lastFile);
-		}
-		modTimes.add(valueOf(fsTick(lastFile)));
-		for (int i = 0; i < 10; i++) {
-			lastFile = new File(db.getWorkTree(), "2." + i);
-			FileUtils.createNewFile(lastFile);
-			if (i % 4 == 0)
-				fsTick(lastFile);
-		}
-		FileTreeIteratorWithTimeControl fileIt = new FileTreeIteratorWithTimeControl(
-				db, modTimes);
-		try (NameConflictTreeWalk tw = new NameConflictTreeWalk(db)) {
-			tw.addTree(fileIt);
-			tw.setRecursive(true);
-			FileTreeIterator t;
-			long t0 = 0;
-			for (int i = 0; i < 10; i++) {
-				assertTrue(tw.next());
-				t = tw.getTree(0, FileTreeIterator.class);
-				if (i == 0) {
-					t0 = t.getEntryLastModified();
-				} else {
-					assertEquals(t0, t.getEntryLastModified());
-				}
-			}
-			long t1 = 0;
-			for (int i = 0; i < 10; i++) {
-				assertTrue(tw.next());
-				t = tw.getTree(0, FileTreeIterator.class);
-				if (i == 0) {
-					t1 = t.getEntryLastModified();
-					assertTrue(t1 > t0);
-				} else {
-					assertEquals(t1, t.getEntryLastModified());
-				}
-			}
-			long t2 = 0;
-			for (int i = 0; i < 10; i++) {
-				assertTrue(tw.next());
-				t = tw.getTree(0, FileTreeIterator.class);
-				if (i == 0) {
-					t2 = t.getEntryLastModified();
-					assertTrue(t2 > t1);
-				} else {
-					assertEquals(t2, t.getEntryLastModified());
-				}
-			}
-		}
-	}
 
 	@Test
 	public void testRacyGitDetection() throws Exception {
@@ -137,10 +75,10 @@ public class RacyGitTests extends RepositoryTestCase {
 		fsTick(db.getIndexFile());
 
 		// create two files
-		File a = addToWorkDir("a", "a");
-		File b = addToWorkDir("b", "b");
-		assertTrue(a.setLastModified(b.lastModified()));
-		assertTrue(b.setLastModified(b.lastModified()));
+		File a = writeToWorkDir("a", "a");
+		File b = writeToWorkDir("b", "b");
+		TimeUtil.setLastModifiedOf(a.toPath(), b.toPath());
+		TimeUtil.setLastModifiedOf(b.toPath(), b.toPath());
 
 		// wait to ensure that file-modTimes and therefore index entry modTime
 		// doesn't match the modtime of index-file after next persistance
@@ -158,23 +96,36 @@ public class RacyGitTests extends RepositoryTestCase {
 		fsTick(db.getIndexFile());
 
 		// Create a racy git situation. This is a situation that the index is
-		// updated and then a file is modified within a second. By changing the
-		// index file artificially, we create a fake racy situation.
-		File updatedA = addToWorkDir("a", "a2");
-		assertTrue(updatedA.setLastModified(updatedA.lastModified() + 100));
+		// updated and then a file is modified within the same tick of the
+		// filesystem timestamp resolution. By changing the index file
+		// artificially, we create a fake racy situation.
+		File updatedA = writeToWorkDir("a", "a2");
+		Instant newLastModified = TimeUtil
+				.setLastModifiedWithOffset(updatedA.toPath(), 100L);
 		resetIndex(new FileTreeIterator(db));
-		assertTrue(db.getIndexFile()
-				.setLastModified(updatedA.lastModified() + 90));
+		FS.DETECTED.setLastModified(db.getIndexFile().toPath(),
+				newLastModified);
 
-		db.readDirCache();
-		// although racily clean a should not be reported as being dirty
+		DirCache dc = db.readDirCache();
+		// check index state: although racily clean a should not be reported as
+		// being dirty since we forcefully reset the index to match the working
+		// tree
 		assertEquals(
 				"[a, mode:100644, time:t1, smudged, length:0, content:a2]"
 						+ "[b, mode:100644, time:t0, length:1, content:b]",
 				indexState(SMUDGE | MOD_TIME | LENGTH | CONTENT));
+
+		// compare state of files in working tree with index to check that
+		// FileTreeIterator.isModified() works as expected
+		FileTreeIterator f = new FileTreeIterator(db.getWorkTree(), db.getFS(),
+				db.getConfig().get(WorkingTreeOptions.KEY));
+		assertTrue(f.findFile("a"));
+		try (ObjectReader reader = db.newObjectReader()) {
+			assertFalse(f.isModified(dc.getEntry("a"), false, reader));
+		}
 	}
 
-	private File addToWorkDir(String path, String content) throws IOException {
+	private File writeToWorkDir(String path, String content) throws IOException {
 		File f = new File(db.getWorkTree(), path);
 		try (FileOutputStream fos = new FileOutputStream(f)) {
 			fos.write(content.getBytes(UTF_8));

org.eclipse.jgit.test/tst/org/eclipse/jgit/merge/MergerTest.java

@@ -43,6 +43,7 @@
 package org.eclipse.jgit.merge;
 
 import static java.nio.charset.StandardCharsets.UTF_8;
+import static java.time.Instant.EPOCH;
 import static org.eclipse.jgit.lib.Constants.OBJ_BLOB;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertFalse;
@@ -54,6 +55,7 @@ import java.io.ByteArrayOutputStream;
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.IOException;
+import java.time.Instant;
 import java.util.Arrays;
 import java.util.Map;
 
@@ -840,9 +842,9 @@ public class MergerTest extends RepositoryTestCase {
 	 * Throws an exception if reading beyond limit.
 	 */
 	static class BigReadForbiddenStream extends ObjectStream.Filter {
-		int limit;
+		long limit;
 
-		BigReadForbiddenStream(ObjectStream orig, int limit) {
+		BigReadForbiddenStream(ObjectStream orig, long limit) {
 			super(orig.getType(), orig.getSize(), orig);
 			this.limit = limit;
 		}
@@ -1090,13 +1092,13 @@ public class MergerTest extends RepositoryTestCase {
 	@Theory
 	public void checkForCorrectIndex(MergeStrategy strategy) throws Exception {
 		File f;
-		long lastTs4, lastTsIndex;
+		Instant lastTs4, lastTsIndex;
 		Git git = Git.wrap(db);
 		File indexFile = db.getIndexFile();
 
 		// Create initial content and remember when the last file was written.
 		f = writeTrashFiles(false, "orig", "orig", "1\n2\n3", "orig", "orig");
-		lastTs4 = FS.DETECTED.lastModified(f);
+		lastTs4 = FS.DETECTED.lastModifiedInstant(f);
 
 		// add all files, commit and check this doesn't update any working tree
 		// files and that the index is in a new file system timer tick. Make
@@ -1109,8 +1111,9 @@ public class MergerTest extends RepositoryTestCase {
 		checkConsistentLastModified("0", "1", "2", "3", "4");
 		checkModificationTimeStampOrder("1", "2", "3", "4", "<.git/index");
 		assertEquals("Commit should not touch working tree file 4", lastTs4,
-				FS.DETECTED.lastModified(new File(db.getWorkTree(), "4")));
-		lastTsIndex = FS.DETECTED.lastModified(indexFile);
+				FS.DETECTED
+						.lastModifiedInstant(new File(db.getWorkTree(), "4")));
+		lastTsIndex = FS.DETECTED.lastModifiedInstant(indexFile);
 
 		// Do modifications on the master branch. Then add and commit. This
 		// should touch only "0", "2 and "3"
@@ -1124,7 +1127,7 @@ public class MergerTest extends RepositoryTestCase {
 		checkConsistentLastModified("0", "1", "2", "3", "4");
 		checkModificationTimeStampOrder("1", "4", "*" + lastTs4, "<*"
 				+ lastTsIndex, "<0", "2", "3", "<.git/index");
-		lastTsIndex = FS.DETECTED.lastModified(indexFile);
+		lastTsIndex = FS.DETECTED.lastModifiedInstant(indexFile);
 
 		// Checkout a side branch. This should touch only "0", "2 and "3"
 		fsTick(indexFile);
@@ -1133,7 +1136,7 @@ public class MergerTest extends RepositoryTestCase {
 		checkConsistentLastModified("0", "1", "2", "3", "4");
 		checkModificationTimeStampOrder("1", "4", "*" + lastTs4, "<*"
 				+ lastTsIndex, "<0", "2", "3", ".git/index");
-		lastTsIndex = FS.DETECTED.lastModified(indexFile);
+		lastTsIndex = FS.DETECTED.lastModifiedInstant(indexFile);
 
 		// This checkout may have populated worktree and index so fast that we
 		// may have smudged entries now. Check that we have the right content
@@ -1146,13 +1149,13 @@ public class MergerTest extends RepositoryTestCase {
 				indexState(CONTENT));
 		fsTick(indexFile);
 		f = writeTrashFiles(false, "orig", "orig", "1\n2\n3", "orig", "orig");
-		lastTs4 = FS.DETECTED.lastModified(f);
+		lastTs4 = FS.DETECTED.lastModifiedInstant(f);
 		fsTick(f);
 		git.add().addFilepattern(".").call();
 		checkConsistentLastModified("0", "1", "2", "3", "4");
 		checkModificationTimeStampOrder("*" + lastTsIndex, "<0", "1", "2", "3",
 				"4", "<.git/index");
-		lastTsIndex = FS.DETECTED.lastModified(indexFile);
+		lastTsIndex = FS.DETECTED.lastModifiedInstant(indexFile);
 
 		// Do modifications on the side branch. Touch only "1", "2 and "3"
 		fsTick(indexFile);
@@ -1163,7 +1166,7 @@ public class MergerTest extends RepositoryTestCase {
 		checkConsistentLastModified("0", "1", "2", "3", "4");
 		checkModificationTimeStampOrder("0", "4", "*" + lastTs4, "<*"
 				+ lastTsIndex, "<1", "2", "3", "<.git/index");
-		lastTsIndex = FS.DETECTED.lastModified(indexFile);
+		lastTsIndex = FS.DETECTED.lastModifiedInstant(indexFile);
 
 		// merge master and side. Should only touch "0," "2" and "3"
 		fsTick(indexFile);
@@ -1330,9 +1333,10 @@ public class MergerTest extends RepositoryTestCase {
 			assertEquals(
 					"IndexEntry with path "
 							+ path
-							+ " has lastmodified with is different from the worktree file",
-					FS.DETECTED.lastModified(new File(workTree, path)), dc.getEntry(path)
-							.getLastModified());
+							+ " has lastmodified which is different from the worktree file",
+					FS.DETECTED.lastModifiedInstant(new File(workTree, path)),
+					dc.getEntry(path)
+							.getLastModifiedInstant());
 	}
 
 	// Assert that modification timestamps of working tree files are as
@@ -1341,21 +1345,22 @@ public class MergerTest extends RepositoryTestCase {
 	// then this file must be younger then file i. A path "*<modtime>"
 	// represents a file with a modification time of <modtime>
 	// E.g. ("a", "b", "<c", "f/a.txt") means: a<=b<c<=f/a.txt
-	private void checkModificationTimeStampOrder(String... pathes)
-			throws IOException {
-		long lastMod = Long.MIN_VALUE;
+	private void checkModificationTimeStampOrder(String... pathes) {
+		Instant lastMod = EPOCH;
 		for (String p : pathes) {
 			boolean strong = p.startsWith("<");
 			boolean fixed = p.charAt(strong ? 1 : 0) == '*';
 			p = p.substring((strong ? 1 : 0) + (fixed ? 1 : 0));
-			long curMod = fixed ? Long.valueOf(p).longValue()
-					: FS.DETECTED.lastModified(new File(db.getWorkTree(), p));
-			if (strong)
+			Instant curMod = fixed ? Instant.parse(p)
+					: FS.DETECTED
+							.lastModifiedInstant(new File(db.getWorkTree(), p));
+			if (strong) {
 				assertTrue("path " + p + " is not younger than predecesssor",
-						curMod > lastMod);
-			else
+						curMod.compareTo(lastMod) > 0);
+			} else {
 				assertTrue("path " + p + " is older than predecesssor",
-						curMod >= lastMod);
+						curMod.compareTo(lastMod) >= 0);
+			}
 		}
 	}
 

org.eclipse.jgit.test/tst/org/eclipse/jgit/revwalk/RevObjectTest.java

@@ -89,8 +89,8 @@ public class RevObjectTest extends RevWalkTestCase {
 		assertEquals(a1.hashCode(), a2.hashCode());
 		assertEquals(b1.hashCode(), b2.hashCode());
 
-		assertTrue(AnyObjectId.equals(a1, a2));
-		assertTrue(AnyObjectId.equals(b1, b2));
+		assertTrue(AnyObjectId.isEqual(a1, a2));
+		assertTrue(AnyObjectId.isEqual(b1, b2));
 	}
 
 	@Test

org.eclipse.jgit.test/tst/org/eclipse/jgit/storage/file/FileBasedConfigTest.java

@@ -46,12 +46,13 @@ import static java.nio.charset.StandardCharsets.UTF_8;
 import static org.eclipse.jgit.util.FileUtils.pathToString;
 import static org.junit.Assert.assertArrayEquals;
 import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
 
 import java.io.ByteArrayOutputStream;
-import java.io.File;
-import java.io.FileOutputStream;
 import java.io.IOException;
+import java.io.OutputStream;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.StandardOpenOption;
 import java.util.StringTokenizer;
 
 import org.eclipse.jgit.errors.ConfigInvalidException;
@@ -85,42 +86,44 @@ public class FileBasedConfigTest {
 	private static final String CONTENT3 = "[" + USER + "]\n\t" + NAME + " = "
 			+ ALICE + "\n" + "[" + USER + "]\n\t" + EMAIL + " = " + ALICE_EMAIL;
 
-	private File trash;
+	private Path trash;
 
 	@Before
 	public void setUp() throws Exception {
-		trash = File.createTempFile("tmp_", "");
-		trash.delete();
-		assertTrue("mkdir " + trash, trash.mkdir());
+		trash = Files.createTempDirectory("tmp_");
+		FS.getFileStoreAttributes(trash.getParent());
 	}
 
 	@After
 	public void tearDown() throws Exception {
-		FileUtils.delete(trash, FileUtils.RECURSIVE | FileUtils.SKIP_MISSING);
+		FileUtils.delete(trash.toFile(),
+				FileUtils.RECURSIVE | FileUtils.SKIP_MISSING | FileUtils.RETRY);
 	}
 
 	@Test
 	public void testSystemEncoding() throws IOException, ConfigInvalidException {
-		final File file = createFile(CONTENT1.getBytes(UTF_8));
-		final FileBasedConfig config = new FileBasedConfig(file, FS.DETECTED);
+		final Path file = createFile(CONTENT1.getBytes(UTF_8));
+		final FileBasedConfig config = new FileBasedConfig(file.toFile(),
+				FS.DETECTED);
 		config.load();
 		assertEquals(ALICE, config.getString(USER, null, NAME));
 
 		config.setString(USER, null, NAME, BOB);
 		config.save();
-		assertArrayEquals(CONTENT2.getBytes(UTF_8), IO.readFully(file));
+		assertArrayEquals(CONTENT2.getBytes(UTF_8), IO.readFully(file.toFile()));
 	}
 
 	@Test
 	public void testUTF8withoutBOM() throws IOException, ConfigInvalidException {
-		final File file = createFile(CONTENT1.getBytes(UTF_8));
-		final FileBasedConfig config = new FileBasedConfig(file, FS.DETECTED);
+		final Path file = createFile(CONTENT1.getBytes(UTF_8));
+		final FileBasedConfig config = new FileBasedConfig(file.toFile(),
+				FS.DETECTED);
 		config.load();
 		assertEquals(ALICE, config.getString(USER, null, NAME));
 
 		config.setString(USER, null, NAME, BOB);
 		config.save();
-		assertArrayEquals(CONTENT2.getBytes(UTF_8), IO.readFully(file));
+		assertArrayEquals(CONTENT2.getBytes(UTF_8), IO.readFully(file.toFile()));
 	}
 
 	@Test
@@ -131,8 +134,9 @@ public class FileBasedConfigTest {
 		bos1.write(0xBF);
 		bos1.write(CONTENT1.getBytes(UTF_8));
 
-		final File file = createFile(bos1.toByteArray());
-		final FileBasedConfig config = new FileBasedConfig(file, FS.DETECTED);
+		final Path file = createFile(bos1.toByteArray());
+		final FileBasedConfig config = new FileBasedConfig(file.toFile(),
+				FS.DETECTED);
 		config.load();
 		assertEquals(ALICE, config.getString(USER, null, NAME));
 
@@ -144,7 +148,7 @@ public class FileBasedConfigTest {
 		bos2.write(0xBB);
 		bos2.write(0xBF);
 		bos2.write(CONTENT2.getBytes(UTF_8));
-		assertArrayEquals(bos2.toByteArray(), IO.readFully(file));
+		assertArrayEquals(bos2.toByteArray(), IO.readFully(file.toFile()));
 	}
 
 	@Test
@@ -153,8 +157,9 @@ public class FileBasedConfigTest {
 		bos1.write(" \n\t".getBytes(UTF_8));
 		bos1.write(CONTENT1.getBytes(UTF_8));
 
-		final File file = createFile(bos1.toByteArray());
-		final FileBasedConfig config = new FileBasedConfig(file, FS.DETECTED);
+		final Path file = createFile(bos1.toByteArray());
+		final FileBasedConfig config = new FileBasedConfig(file.toFile(),
+				FS.DETECTED);
 		config.load();
 		assertEquals(ALICE, config.getString(USER, null, NAME));
 
@@ -164,19 +169,20 @@ public class FileBasedConfigTest {
 		final ByteArrayOutputStream bos2 = new ByteArrayOutputStream();
 		bos2.write(" \n\t".getBytes(UTF_8));
 		bos2.write(CONTENT2.getBytes(UTF_8));
-		assertArrayEquals(bos2.toByteArray(), IO.readFully(file));
+		assertArrayEquals(bos2.toByteArray(), IO.readFully(file.toFile()));
 	}
 
 	@Test
 	public void testIncludeAbsolute()
 			throws IOException, ConfigInvalidException {
-		final File includedFile = createFile(CONTENT1.getBytes(UTF_8));
+		final Path includedFile = createFile(CONTENT1.getBytes(UTF_8));
 		final ByteArrayOutputStream bos = new ByteArrayOutputStream();
 		bos.write("[include]\npath=".getBytes(UTF_8));
-		bos.write(pathToString(includedFile).getBytes(UTF_8));
+		bos.write(pathToString(includedFile.toFile()).getBytes(UTF_8));
 
-		final File file = createFile(bos.toByteArray());
-		final FileBasedConfig config = new FileBasedConfig(file, FS.DETECTED);
+		final Path file = createFile(bos.toByteArray());
+		final FileBasedConfig config = new FileBasedConfig(file.toFile(),
+				FS.DETECTED);
 		config.load();
 		assertEquals(ALICE, config.getString(USER, null, NAME));
 	}
@@ -184,13 +190,14 @@ public class FileBasedConfigTest {
 	@Test
 	public void testIncludeRelativeDot()
 			throws IOException, ConfigInvalidException {
-		final File includedFile = createFile(CONTENT1.getBytes(UTF_8), "dir1");
+		final Path includedFile = createFile(CONTENT1.getBytes(UTF_8), "dir1");
 		final ByteArrayOutputStream bos = new ByteArrayOutputStream();
 		bos.write("[include]\npath=".getBytes(UTF_8));
-		bos.write(("./" + includedFile.getName()).getBytes(UTF_8));
+		bos.write(("./" + includedFile.getFileName()).getBytes(UTF_8));
 
-		final File file = createFile(bos.toByteArray(), "dir1");
-		final FileBasedConfig config = new FileBasedConfig(file, FS.DETECTED);
+		final Path file = createFile(bos.toByteArray(), "dir1");
+		final FileBasedConfig config = new FileBasedConfig(file.toFile(),
+				FS.DETECTED);
 		config.load();
 		assertEquals(ALICE, config.getString(USER, null, NAME));
 	}
@@ -198,14 +205,15 @@ public class FileBasedConfigTest {
 	@Test
 	public void testIncludeRelativeDotDot()
 			throws IOException, ConfigInvalidException {
-		final File includedFile = createFile(CONTENT1.getBytes(UTF_8), "dir1");
+		final Path includedFile = createFile(CONTENT1.getBytes(UTF_8), "dir1");
 		final ByteArrayOutputStream bos = new ByteArrayOutputStream();
 		bos.write("[include]\npath=".getBytes(UTF_8));
-		bos.write(("../" + includedFile.getParentFile().getName() + "/"
-				+ includedFile.getName()).getBytes(UTF_8));
+		bos.write(("../" + includedFile.getParent().getFileName() + "/"
+				+ includedFile.getFileName()).getBytes(UTF_8));
 
-		final File file = createFile(bos.toByteArray(), "dir2");
-		final FileBasedConfig config = new FileBasedConfig(file, FS.DETECTED);
+		final Path file = createFile(bos.toByteArray(), "dir2");
+		final FileBasedConfig config = new FileBasedConfig(file.toFile(),
+				FS.DETECTED);
 		config.load();
 		assertEquals(ALICE, config.getString(USER, null, NAME));
 	}
@@ -213,13 +221,14 @@ public class FileBasedConfigTest {
 	@Test
 	public void testIncludeRelativeDotDotNotFound()
 			throws IOException, ConfigInvalidException {
-		final File includedFile = createFile(CONTENT1.getBytes(UTF_8));
+		final Path includedFile = createFile(CONTENT1.getBytes(UTF_8));
 		final ByteArrayOutputStream bos = new ByteArrayOutputStream();
 		bos.write("[include]\npath=".getBytes(UTF_8));
-		bos.write(("../" + includedFile.getName()).getBytes(UTF_8));
+		bos.write(("../" + includedFile.getFileName()).getBytes(UTF_8));
 
-		final File file = createFile(bos.toByteArray());
-		final FileBasedConfig config = new FileBasedConfig(file, FS.DETECTED);
+		final Path file = createFile(bos.toByteArray());
+		final FileBasedConfig config = new FileBasedConfig(file.toFile(),
+				FS.DETECTED);
 		config.load();
 		assertEquals(null, config.getString(USER, null, NAME));
 	}
@@ -227,16 +236,16 @@ public class FileBasedConfigTest {
 	@Test
 	public void testIncludeWithTilde()
 			throws IOException, ConfigInvalidException {
-		final File includedFile = createFile(CONTENT1.getBytes(UTF_8), "home");
+		final Path includedFile = createFile(CONTENT1.getBytes(UTF_8), "home");
 		final ByteArrayOutputStream bos = new ByteArrayOutputStream();
 		bos.write("[include]\npath=".getBytes(UTF_8));
-		bos.write(("~/" + includedFile.getName()).getBytes(UTF_8));
+		bos.write(("~/" + includedFile.getFileName()).getBytes(UTF_8));
 
-		final File file = createFile(bos.toByteArray(), "repo");
+		final Path file = createFile(bos.toByteArray(), "repo");
 		final FS fs = FS.DETECTED.newInstance();
-		fs.setUserHome(includedFile.getParentFile());
+		fs.setUserHome(includedFile.getParent().toFile());
 
-		final FileBasedConfig config = new FileBasedConfig(file, fs);
+		final FileBasedConfig config = new FileBasedConfig(file.toFile(), fs);
 		config.load();
 		assertEquals(ALICE, config.getString(USER, null, NAME));
 	}
@@ -246,13 +255,14 @@ public class FileBasedConfigTest {
 			throws IOException, ConfigInvalidException {
 		// use a content with multiple sections and multiple key/value pairs
 		// because code for first line works different than for subsequent lines
-		final File includedFile = createFile(CONTENT3.getBytes(UTF_8), "dir1");
+		final Path includedFile = createFile(CONTENT3.getBytes(UTF_8), "dir1");
 
-		final File file = createFile(new byte[0], "dir2");
-		FileBasedConfig config = new FileBasedConfig(file, FS.DETECTED);
+		final Path file = createFile(new byte[0], "dir2");
+		FileBasedConfig config = new FileBasedConfig(file.toFile(),
+				FS.DETECTED);
 		config.setString("include", null, "path",
-				("../" + includedFile.getParentFile().getName() + "/"
-						+ includedFile.getName()));
+				("../" + includedFile.getParent().getFileName() + "/"
+						+ includedFile.getFileName()));
 
 		// just by setting the include.path, it won't be included
 		assertEquals(null, config.getString(USER, null, NAME));
@@ -267,7 +277,7 @@ public class FileBasedConfigTest {
 		assertEquals(2,
 				new StringTokenizer(expectedText, "\n", false).countTokens());
 
-		config = new FileBasedConfig(file, FS.DETECTED);
+		config = new FileBasedConfig(file.toFile(), FS.DETECTED);
 		config.load();
 
 		String actualText = config.toText();
@@ -285,16 +295,17 @@ public class FileBasedConfigTest {
 		assertEquals(ALICE_EMAIL, config.getString(USER, null, EMAIL));
 	}
 
-	private File createFile(byte[] content) throws IOException {
+	private Path createFile(byte[] content) throws IOException {
 		return createFile(content, null);
 	}
 
-	private File createFile(byte[] content, String subdir) throws IOException {
-		File dir = subdir != null ? new File(trash, subdir) : trash;
-		dir.mkdirs();
+	private Path createFile(byte[] content, String subdir) throws IOException {
+		Path dir = subdir != null ? trash.resolve(subdir) : trash;
+		Files.createDirectories(dir);
 
-		File f = File.createTempFile(getClass().getName(), null, dir);
-		try (FileOutputStream os = new FileOutputStream(f, true)) {
+		Path f = Files.createTempFile(dir, getClass().getName(), null);
+		try (OutputStream os = Files.newOutputStream(f,
+				StandardOpenOption.APPEND)) {
 			os.write(content);
 		}
 		return f;

org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/OpenSshConfigTest.java

@@ -56,10 +56,13 @@ import java.io.File;
 import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.OutputStreamWriter;
+import java.time.Instant;
+import java.util.concurrent.TimeUnit;
 
 import org.eclipse.jgit.junit.RepositoryTestCase;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.transport.OpenSshConfig.Host;
+import org.eclipse.jgit.util.FS;
 import org.eclipse.jgit.util.FileUtils;
 import org.eclipse.jgit.util.SystemReader;
 import org.junit.Before;
@@ -91,13 +94,19 @@ public class OpenSshConfigTest extends RepositoryTestCase {
 	}
 
 	private void config(String data) throws IOException {
-		long lastMtime = configFile.lastModified();
+		FS fs = FS.DETECTED;
+		long resolution = FS.getFileStoreAttributes(configFile.toPath())
+				.getFsTimestampResolution().toNanos();
+		Instant lastMtime = fs.lastModifiedInstant(configFile);
 		do {
 			try (final OutputStreamWriter fw = new OutputStreamWriter(
 					new FileOutputStream(configFile), UTF_8)) {
 				fw.write(data);
+				TimeUnit.NANOSECONDS.sleep(resolution);
+			} catch (InterruptedException e) {
+				Thread.interrupted();
 			}
-		} while (lastMtime == configFile.lastModified());
+		} while (lastMtime.equals(fs.lastModifiedInstant(configFile)));
 	}
 
 	@Test

org.eclipse.jgit.test/tst/org/eclipse/jgit/treewalk/FileTreeIteratorTest.java

@@ -54,6 +54,7 @@ import java.io.File;
 import java.io.IOException;
 import java.nio.file.InvalidPathException;
 import java.security.MessageDigest;
+import java.time.Instant;
 
 import org.eclipse.jgit.api.Git;
 import org.eclipse.jgit.api.ResetCommand.ResetType;
@@ -88,7 +89,7 @@ import org.junit.Test;
 public class FileTreeIteratorTest extends RepositoryTestCase {
 	private final String[] paths = { "a,", "a,b", "a/b", "a0b" };
 
-	private long[] mtime;
+	private Instant[] mtime;
 
 	@Override
 	@Before
@@ -101,11 +102,11 @@ public class FileTreeIteratorTest extends RepositoryTestCase {
 		// This should stress the sorting code better than doing it in
 		// the correct order.
 		//
-		mtime = new long[paths.length];
+		mtime = new Instant[paths.length];
 		for (int i = paths.length - 1; i >= 0; i--) {
 			final String s = paths[i];
 			writeTrashFile(s, s);
-			mtime[i] = FS.DETECTED.lastModified(new File(trash, s));
+			mtime[i] = db.getFS().lastModifiedInstant(new File(trash, s));
 		}
 	}
 
@@ -201,7 +202,7 @@ public class FileTreeIteratorTest extends RepositoryTestCase {
 		assertEquals(FileMode.REGULAR_FILE.getBits(), top.mode);
 		assertEquals(paths[0], nameOf(top));
 		assertEquals(paths[0].length(), top.getEntryLength());
-		assertEquals(mtime[0], top.getEntryLastModified());
+		assertEquals(mtime[0], top.getEntryLastModifiedInstant());
 
 		top.next(1);
 		assertFalse(top.first());
@@ -209,7 +210,7 @@ public class FileTreeIteratorTest extends RepositoryTestCase {
 		assertEquals(FileMode.REGULAR_FILE.getBits(), top.mode);
 		assertEquals(paths[1], nameOf(top));
 		assertEquals(paths[1].length(), top.getEntryLength());
-		assertEquals(mtime[1], top.getEntryLastModified());
+		assertEquals(mtime[1], top.getEntryLastModifiedInstant());
 
 		top.next(1);
 		assertFalse(top.first());
@@ -224,7 +225,7 @@ public class FileTreeIteratorTest extends RepositoryTestCase {
 		assertFalse(sub.eof());
 		assertEquals(paths[2], nameOf(sub));
 		assertEquals(paths[2].length(), subfti.getEntryLength());
-		assertEquals(mtime[2], subfti.getEntryLastModified());
+		assertEquals(mtime[2], subfti.getEntryLastModifiedInstant());
 
 		sub.next(1);
 		assertTrue(sub.eof());
@@ -235,7 +236,7 @@ public class FileTreeIteratorTest extends RepositoryTestCase {
 		assertEquals(FileMode.REGULAR_FILE.getBits(), top.mode);
 		assertEquals(paths[3], nameOf(top));
 		assertEquals(paths[3].length(), top.getEntryLength());
-		assertEquals(mtime[3], top.getEntryLastModified());
+		assertEquals(mtime[3], top.getEntryLastModifiedInstant());
 
 		top.next(1);
 		assertTrue(top.eof());
@@ -347,20 +348,21 @@ public class FileTreeIteratorTest extends RepositoryTestCase {
 	@Test
 	public void testIsModifiedFileSmudged() throws Exception {
 		File f = writeTrashFile("file", "content");
+		FS fs = db.getFS();
 		try (Git git = new Git(db)) {
 			// The idea of this test is to check the smudged handling
 			// Hopefully fsTick will make sure our entry gets smudged
 			fsTick(f);
 			writeTrashFile("file", "content");
-			long lastModified = f.lastModified();
+			Instant lastModified = fs.lastModifiedInstant(f);
 			git.add().addFilepattern("file").call();
 			writeTrashFile("file", "conten2");
-			f.setLastModified(lastModified);
+			fs.setLastModified(f.toPath(), lastModified);
 			// We cannot trust this to go fast enough on
 			// a system with less than one-second lastModified
 			// resolution, so we force the index to have the
 			// same timestamp as the file we look at.
-			db.getIndexFile().setLastModified(lastModified);
+			fs.setLastModified(db.getIndexFile().toPath(), lastModified);
 		}
 		DirCacheEntry dce = db.readDirCache().getEntry("file");
 		FileTreeIterator fti = new FileTreeIterator(trash, db.getFS(), db

org.eclipse.jgit.test/tst/org/eclipse/jgit/treewalk/FileTreeIteratorWithTimeControl.java

@@ -1,109 +0,0 @@
-/*
- * Copyright (C) 2010, Christian Halstrick <christian.halstrick@sap.com>
- * and other copyright owners as documented in the project's IP log.
- *
- * This program and the accompanying materials are made available
- * under the terms of the Eclipse Distribution License v1.0 which
- * accompanies this distribution, is reproduced below, and is
- * available at http://www.eclipse.org/org/documents/edl-v10.php
- *
- * All rights reserved.
- *
- * Redistribution and use in source and binary forms, with or
- * without modification, are permitted provided that the following
- * conditions are met:
- *
- * - Redistributions of source code must retain the above copyright
- *   notice, this list of conditions and the following disclaimer.
- *
- * - Redistributions in binary form must reproduce the above
- *   copyright notice, this list of conditions and the following
- *   disclaimer in the documentation and/or other materials provided
- *   with the distribution.
- *
- * - Neither the name of the Eclipse Foundation, Inc. nor the
- *   names of its contributors may be used to endorse or promote
- *   products derived from this software without specific prior
- *   written permission.
- *
- * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
- * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
- * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
- * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
- * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
- * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
- * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
- * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
- * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
- * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
- */
-package org.eclipse.jgit.treewalk;
-
-import java.io.File;
-import java.util.SortedSet;
-import java.util.TreeSet;
-
-import org.eclipse.jgit.lib.Config;
-import org.eclipse.jgit.lib.ObjectReader;
-import org.eclipse.jgit.lib.Repository;
-import org.eclipse.jgit.util.FS;
-
-/**
- * A {@link FileTreeIterator} used in tests which allows to specify explicitly
- * what will be returned by {@link #getEntryLastModified()}. This allows to
- * write tests where certain files have to have the same modification time.
- * <p>
- * This iterator is configured by a list of strictly increasing long values
- * t(0), t(1), ..., t(n). For each file with a modification between t(x) and
- * t(x+1) [ t(x) &lt;= time &lt; t(x+1) ] this iterator will report t(x). For
- * files with a modification time smaller t(0) a modification time of 0 is
- * returned. For files with a modification time greater or equal t(n) t(n) will
- * be returned.
- * <p>
- * This class was written especially to test racy-git problems
- */
-public class FileTreeIteratorWithTimeControl extends FileTreeIterator {
-	private TreeSet<Long> modTimes;
-
-	public FileTreeIteratorWithTimeControl(FileTreeIterator p, Repository repo,
-			TreeSet<Long> modTimes) {
-		super(p, repo.getWorkTree(), repo.getFS());
-		this.modTimes = modTimes;
-	}
-
-	public FileTreeIteratorWithTimeControl(FileTreeIterator p, File f, FS fs,
-			TreeSet<Long> modTimes) {
-		super(p, f, fs);
-		this.modTimes = modTimes;
-	}
-
-	public FileTreeIteratorWithTimeControl(Repository repo,
-			TreeSet<Long> modTimes) {
-		super(repo);
-		this.modTimes = modTimes;
-	}
-
-	public FileTreeIteratorWithTimeControl(File f, FS fs,
-			TreeSet<Long> modTimes) {
-		super(f, fs, new Config().get(WorkingTreeOptions.KEY));
-		this.modTimes = modTimes;
-	}
-
-	@Override
-	public AbstractTreeIterator createSubtreeIterator(ObjectReader reader) {
-		return new FileTreeIteratorWithTimeControl(this,
-				((FileEntry) current()).getFile(), fs, modTimes);
-	}
-
-	@Override
-	public long getEntryLastModified() {
-		if (modTimes == null)
-			return 0;
-		Long cutOff = Long.valueOf(super.getEntryLastModified() + 1);
-		SortedSet<Long> head = modTimes.headSet(cutOff);
-		return head.isEmpty() ? 0 : head.last().longValue();
-	}
-}

org.eclipse.jgit.test/tst/org/eclipse/jgit/util/FSTest.java

@@ -43,6 +43,7 @@
 
 package org.eclipse.jgit.util;
 
+import static java.time.Instant.EPOCH;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertTrue;
@@ -67,6 +68,7 @@ import java.util.concurrent.TimeUnit;
 
 import org.eclipse.jgit.errors.CommandFailedException;
 import org.eclipse.jgit.junit.RepositoryTestCase;
+import org.eclipse.jgit.lib.RepositoryCache;
 import org.junit.After;
 import org.junit.Assume;
 import org.junit.Before;
@@ -107,7 +109,7 @@ public class FSTest {
 		assertTrue(fs.exists(link));
 		String targetName = fs.readSymLink(link);
 		assertEquals("b", targetName);
-		assertTrue(fs.lastModified(link) > 0);
+		assertTrue(fs.lastModifiedInstant(link).compareTo(EPOCH) > 0);
 		assertTrue(fs.exists(link));
 		assertFalse(fs.canExecute(link));
 		// The length of a symbolic link is a length of the target file path.
@@ -121,8 +123,9 @@ public class FSTest {
 		// Now create the link target
 		FileUtils.createNewFile(target);
 		assertTrue(fs.exists(link));
-		assertTrue(fs.lastModified(link) > 0);
-		assertTrue(fs.lastModified(target) > fs.lastModified(link));
+		assertTrue(fs.lastModifiedInstant(link).compareTo(EPOCH) > 0);
+		assertTrue(fs.lastModifiedInstant(target)
+				.compareTo(fs.lastModifiedInstant(link)) > 0);
 		assertFalse(fs.canExecute(link));
 		fs.setExecute(target, true);
 		assertFalse(fs.canExecute(link));
@@ -229,7 +232,8 @@ public class FSTest {
 				.ofPattern("uuuu-MMM-dd HH:mm:ss.nnnnnnnnn", Locale.ENGLISH)
 				.withZone(ZoneId.systemDefault());
 		Path dir = Files.createTempDirectory("probe-filesystem");
-		Duration resolution = FS.getFsTimerResolution(dir);
+		Duration resolution = FS.getFileStoreAttributes(dir)
+				.getFsTimestampResolution();
 		long resolutionNs = resolution.toNanos();
 		assertTrue(resolutionNs > 0);
 		for (int i = 0; i < 10; i++) {
@@ -252,4 +256,11 @@ public class FSTest {
 			}
 		}
 	}
+
+	// bug 548682
+	@Test
+	public void testRepoCacheRelativePathUnbornRepo() {
+		assertFalse(RepositoryCache.FileKey
+				.isGitRepository(new File("repo.git"), FS.DETECTED));
+	}
 }

org.eclipse.jgit.test/tst/org/eclipse/jgit/util/SimpleLruCacheTest.java

@@ -0,0 +1,135 @@
+/*
+ * Copyright (C) 2019, Matthias Sohn <matthias.sohn@sap.com>
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+package org.eclipse.jgit.util;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class SimpleLruCacheTest {
+
+	private Path trash;
+
+	private SimpleLruCache<String, String> cache;
+
+
+	@Before
+	public void setup() throws IOException {
+		trash = Files.createTempDirectory("tmp_");
+		cache = new SimpleLruCache<>(100, 0.2f);
+	}
+
+	@Before
+	@After
+	public void tearDown() throws Exception {
+		FileUtils.delete(trash.toFile(),
+				FileUtils.RECURSIVE | FileUtils.SKIP_MISSING);
+	}
+
+	@Test
+	public void testPutGet() {
+		cache.put("a", "A");
+		cache.put("z", "Z");
+		assertEquals("A", cache.get("a"));
+		assertEquals("Z", cache.get("z"));
+	}
+
+	@Test(expected = IllegalArgumentException.class)
+	public void testPurgeFactorTooLarge() {
+		cache.configure(5, 1.01f);
+	}
+
+	@Test(expected = IllegalArgumentException.class)
+	public void testPurgeFactorTooLarge2() {
+		cache.configure(5, 100);
+	}
+
+	@Test(expected = IllegalArgumentException.class)
+	public void testPurgeFactorTooSmall() {
+		cache.configure(5, 0);
+	}
+
+	@Test(expected = IllegalArgumentException.class)
+	public void testPurgeFactorTooSmall2() {
+		cache.configure(5, -100);
+	}
+
+	@Test
+	public void testGetMissing() {
+		assertEquals(null, cache.get("a"));
+	}
+
+	@Test
+	public void testPurge() {
+		for (int i = 0; i < 101; i++) {
+			cache.put("a" + i, "a" + i);
+		}
+		assertEquals(80, cache.size());
+		assertNull(cache.get("a0"));
+		assertNull(cache.get("a20"));
+		assertNotNull(cache.get("a21"));
+		assertNotNull(cache.get("a99"));
+	}
+
+	@Test
+	public void testConfigure() {
+		for (int i = 0; i < 100; i++) {
+			cache.put("a" + i, "a" + i);
+		}
+		assertEquals(100, cache.size());
+		cache.configure(10, 0.3f);
+		assertEquals(7, cache.size());
+		assertNull(cache.get("a0"));
+		assertNull(cache.get("a92"));
+		assertNotNull(cache.get("a93"));
+		assertNotNull(cache.get("a99"));
+	}
+}

org.eclipse.jgit.test/tst/org/eclipse/jgit/util/StatsTest.java

@@ -0,0 +1,137 @@
+/*
+ * Copyright (C) 2019, Matthias Sohn <matthias.sohn@sap.com>
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available
+ * under the terms of the Eclipse Distribution License v1.0 which
+ * accompanies this distribution, is reproduced below, and is
+ * available at http://www.eclipse.org/org/documents/edl-v10.php
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or
+ * without modification, are permitted provided that the following
+ * conditions are met:
+ *
+ * - Redistributions of source code must retain the above copyright
+ *   notice, this list of conditions and the following disclaimer.
+ *
+ * - Redistributions in binary form must reproduce the above
+ *   copyright notice, this list of conditions and the following
+ *   disclaimer in the documentation and/or other materials provided
+ *   with the distribution.
+ *
+ * - Neither the name of the Eclipse Foundation, Inc. nor the
+ *   names of its contributors may be used to endorse or promote
+ *   products derived from this software without specific prior
+ *   written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
+ * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ * STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+package org.eclipse.jgit.util;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+import org.eclipse.jgit.util.Stats;
+import org.junit.Test;
+
+public class StatsTest {
+	@Test
+	public void testStatsTrivial() {
+		Stats s = new Stats();
+		s.add(1);
+		s.add(1);
+		s.add(1);
+		assertEquals(3, s.count());
+		assertEquals(1.0, s.min(), 1E-6);
+		assertEquals(1.0, s.max(), 1E-6);
+		assertEquals(1.0, s.avg(), 1E-6);
+		assertEquals(0.0, s.var(), 1E-6);
+		assertEquals(0.0, s.stddev(), 1E-6);
+	}
+
+	@Test
+	public void testStats() {
+		Stats s = new Stats();
+		s.add(1);
+		s.add(2);
+		s.add(3);
+		s.add(4);
+		assertEquals(4, s.count());
+		assertEquals(1.0, s.min(), 1E-6);
+		assertEquals(4.0, s.max(), 1E-6);
+		assertEquals(2.5, s.avg(), 1E-6);
+		assertEquals(1.666667, s.var(), 1E-6);
+		assertEquals(1.290994, s.stddev(), 1E-6);
+	}
+
+	@Test
+	/**
+	 * see
+	 * https://en.wikipedia.org/wiki/Algorithms_for_calculating_variance#Example
+	 */
+	public void testStatsCancellationExample1() {
+		Stats s = new Stats();
+		s.add(1E8 + 4);
+		s.add(1E8 + 7);
+		s.add(1E8 + 13);
+		s.add(1E8 + 16);
+		assertEquals(4, s.count());
+		assertEquals(1E8 + 4, s.min(), 1E-6);
+		assertEquals(1E8 + 16, s.max(), 1E-6);
+		assertEquals(1E8 + 10, s.avg(), 1E-6);
+		assertEquals(30, s.var(), 1E-6);
+		assertEquals(5.477226, s.stddev(), 1E-6);
+	}
+
+	@Test
+	/**
+	 * see
+	 * https://en.wikipedia.org/wiki/Algorithms_for_calculating_variance#Example
+	 */
+	public void testStatsCancellationExample2() {
+		Stats s = new Stats();
+		s.add(1E9 + 4);
+		s.add(1E9 + 7);
+		s.add(1E9 + 13);
+		s.add(1E9 + 16);
+		assertEquals(4, s.count());
+		assertEquals(1E9 + 4, s.min(), 1E-6);
+		assertEquals(1E9 + 16, s.max(), 1E-6);
+		assertEquals(1E9 + 10, s.avg(), 1E-6);
+		assertEquals(30, s.var(), 1E-6);
+		assertEquals(5.477226, s.stddev(), 1E-6);
+	}
+
+	@Test
+	public void testNoValues() {
+		Stats s = new Stats();
+		assertTrue(Double.isNaN(s.var()));
+		assertTrue(Double.isNaN(s.stddev()));
+		assertTrue(Double.isNaN(s.avg()));
+		assertTrue(Double.isNaN(s.min()));
+		assertTrue(Double.isNaN(s.max()));
+		s.add(42.3);
+		assertTrue(Double.isNaN(s.var()));
+		assertTrue(Double.isNaN(s.stddev()));
+		assertEquals(42.3, s.avg(), 1E-6);
+		assertEquals(42.3, s.max(), 1E-6);
+		assertEquals(42.3, s.min(), 1E-6);
+		s.add(42.3);
+		assertEquals(0, s.var(), 1E-6);
+		assertEquals(0, s.stddev(), 1E-6);
+	}
+}

org.eclipse.jgit.ui/src/org/eclipse/jgit/awtui/CommitGraphPane.java

@@ -64,6 +64,7 @@ import org.eclipse.jgit.awtui.SwingCommitList.SwingLane;
 import org.eclipse.jgit.lib.PersonIdent;
 import org.eclipse.jgit.revplot.PlotCommit;
 import org.eclipse.jgit.revplot.PlotCommitList;
+import org.eclipse.jgit.util.References;
 
 /**
  * Draws a commit graph in a JTable.
@@ -176,7 +177,7 @@ public class CommitGraphPane extends JTable {
 		}
 
 		PersonIdent authorFor(PlotCommit<SwingLane> c) {
-			if (c != lastCommit) {
+			if (!References.isSameObject(c, lastCommit)) {
 				lastCommit = c;
 				lastAuthor = c.getAuthorIdent();
 			}

org.eclipse.jgit/.settings/.api_filters

@@ -0,0 +1,161 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<component id="org.eclipse.jgit" version="2">
+    <resource path="src/org/eclipse/jgit/dircache/DirCacheEntry.java" type="org.eclipse.jgit.dircache.DirCacheEntry">
+        <filter id="1142947843">
+            <message_arguments>
+                <message_argument value="5.1.9"/>
+                <message_argument value="getLastModifiedInstant()"/>
+            </message_arguments>
+        </filter>
+        <filter id="1142947843">
+            <message_arguments>
+                <message_argument value="5.1.9"/>
+                <message_argument value="mightBeRacilyClean(Instant)"/>
+            </message_arguments>
+        </filter>
+        <filter id="1142947843">
+            <message_arguments>
+                <message_argument value="5.1.9"/>
+                <message_argument value="setLastModified(Instant)"/>
+            </message_arguments>
+        </filter>
+    </resource>
+    <resource path="src/org/eclipse/jgit/lib/AnyObjectId.java" type="org.eclipse.jgit.lib.AnyObjectId">
+        <filter id="1141899266">
+            <message_arguments>
+                <message_argument value="5.4"/>
+                <message_argument value="5.5"/>
+                <message_argument value="isEqual(AnyObjectId, AnyObjectId)"/>
+            </message_arguments>
+        </filter>
+    </resource>
+    <resource path="src/org/eclipse/jgit/lib/ConfigConstants.java" type="org.eclipse.jgit.lib.ConfigConstants">
+        <filter id="1142947843">
+            <message_arguments>
+                <message_argument value="5.1.9"/>
+                <message_argument value="CONFIG_FILESYSTEM_SECTION"/>
+            </message_arguments>
+        </filter>
+        <filter id="1142947843">
+            <message_arguments>
+                <message_argument value="5.1.9"/>
+                <message_argument value="CONFIG_KEY_MIN_RACY_THRESHOLD"/>
+            </message_arguments>
+        </filter>
+        <filter id="1142947843">
+            <message_arguments>
+                <message_argument value="5.1.9"/>
+                <message_argument value="CONFIG_KEY_TIMESTAMP_RESOLUTION"/>
+            </message_arguments>
+        </filter>
+    </resource>
+    <resource path="src/org/eclipse/jgit/storage/file/FileBasedConfig.java" type="org.eclipse.jgit.storage.file.FileBasedConfig">
+        <filter id="1142947843">
+            <message_arguments>
+                <message_argument value="5.1.9"/>
+                <message_argument value="load(boolean)"/>
+            </message_arguments>
+        </filter>
+    </resource>
+    <resource path="src/org/eclipse/jgit/treewalk/WorkingTreeIterator.java" type="org.eclipse.jgit.treewalk.WorkingTreeIterator">
+        <filter id="1142947843">
+            <message_arguments>
+                <message_argument value="5.1.9"/>
+                <message_argument value="getEntryLastModifiedInstant()"/>
+            </message_arguments>
+        </filter>
+    </resource>
+    <resource path="src/org/eclipse/jgit/treewalk/WorkingTreeIterator.java" type="org.eclipse.jgit.treewalk.WorkingTreeIterator$Entry">
+        <filter id="336695337">
+            <message_arguments>
+                <message_argument value="org.eclipse.jgit.treewalk.WorkingTreeIterator.Entry"/>
+                <message_argument value="getLastModifiedInstant()"/>
+            </message_arguments>
+        </filter>
+        <filter id="1142947843">
+            <message_arguments>
+                <message_argument value="5.1.9"/>
+                <message_argument value="getLastModifiedInstant()"/>
+            </message_arguments>
+        </filter>
+    </resource>
+    <resource path="src/org/eclipse/jgit/util/FS.java" type="org.eclipse.jgit.util.FS">
+        <filter id="338792546">
+            <message_arguments>
+                <message_argument value="org.eclipse.jgit.util.FS"/>
+                <message_argument value="getFsTimerResolution(Path)"/>
+            </message_arguments>
+        </filter>
+        <filter id="1142947843">
+            <message_arguments>
+                <message_argument value="5.1.9"/>
+                <message_argument value="getFileStoreAttributes(Path)"/>
+            </message_arguments>
+        </filter>
+        <filter id="1142947843">
+            <message_arguments>
+                <message_argument value="5.1.9"/>
+                <message_argument value="lastModifiedInstant(File)"/>
+            </message_arguments>
+        </filter>
+        <filter id="1142947843">
+            <message_arguments>
+                <message_argument value="5.1.9"/>
+                <message_argument value="lastModifiedInstant(Path)"/>
+            </message_arguments>
+        </filter>
+        <filter id="1142947843">
+            <message_arguments>
+                <message_argument value="5.1.9"/>
+                <message_argument value="setAsyncFileStoreAttributes(boolean)"/>
+            </message_arguments>
+        </filter>
+        <filter id="1142947843">
+            <message_arguments>
+                <message_argument value="5.1.9"/>
+                <message_argument value="setLastModified(Path, Instant)"/>
+            </message_arguments>
+        </filter>
+    </resource>
+    <resource path="src/org/eclipse/jgit/util/FS.java" type="org.eclipse.jgit.util.FS$Attributes">
+        <filter id="1142947843">
+            <message_arguments>
+                <message_argument value="5.1.9"/>
+                <message_argument value="getLastModifiedInstant()"/>
+            </message_arguments>
+        </filter>
+    </resource>
+    <resource path="src/org/eclipse/jgit/util/FS.java" type="org.eclipse.jgit.util.FS$FileStoreAttributes">
+        <filter id="1142947843">
+            <message_arguments>
+                <message_argument value="5.1.9"/>
+                <message_argument value="FileStoreAttributes"/>
+            </message_arguments>
+        </filter>
+    </resource>
+    <resource path="src/org/eclipse/jgit/util/References.java" type="org.eclipse.jgit.util.References">
+        <filter id="1108344834">
+            <message_arguments>
+                <message_argument value="5.4"/>
+                <message_argument value="5.5"/>
+                <message_argument value="org.eclipse.jgit.util.References"/>
+            </message_arguments>
+        </filter>
+    </resource>
+    <resource path="src/org/eclipse/jgit/util/SimpleLruCache.java" type="org.eclipse.jgit.util.SimpleLruCache">
+        <filter id="1109393411">
+            <message_arguments>
+                <message_argument value="5.1.9"/>
+                <message_argument value="org.eclipse.jgit.util.SimpleLruCache"/>
+            </message_arguments>
+        </filter>
+    </resource>
+    <resource path="src/org/eclipse/jgit/util/Stats.java" type="org.eclipse.jgit.util.Stats">
+        <filter id="1109393411">
+            <message_arguments>
+                <message_argument value="5.1.9"/>
+                <message_argument value="org.eclipse.jgit.util.Stats"/>
+            </message_arguments>
+        </filter>
+    </resource>
+</component>

org.eclipse.jgit/pom.xml

@@ -223,6 +223,7 @@
         <plugin>
           <groupId>com.github.spotbugs</groupId>
           <artifactId>spotbugs-maven-plugin</artifactId>
+          <version>${spotbugs-maven-plugin-version}</version>
           <configuration>
             <excludeFilterFile>findBugs/FindBugsExcludeFilter.xml</excludeFilterFile>
           </configuration>

org.eclipse.jgit/resources/org/eclipse/jgit/internal/JGitText.properties

@@ -105,6 +105,7 @@ cannotReadObjectsPath=Cannot read {0}/{1}: {2}
 cannotReadTree=Cannot read tree {0}
 cannotRebaseWithoutCurrentHead=Can not rebase without a current HEAD
 cannotResolveLocalTrackingRefForUpdating=Cannot resolve local tracking ref {0} for updating.
+cannotSaveConfig=Cannot save config file ''{0}''
 cannotSquashFixupWithoutPreviousCommit=Cannot {0} without previous commit.
 cannotStoreObjects=cannot store objects
 cannotResolveUniquelyAbbrevObjectId=Could not resolve uniquely the abbreviated object ID
@@ -406,6 +407,7 @@ invalidPathContainsSeparator=Invalid path (contains separator ''{0}''): {1}
 invalidPathPeriodAtEndWindows=Invalid path (period at end is ignored by Windows): {0}
 invalidPathSpaceAtEndWindows=Invalid path (space at end is ignored by Windows): {0}
 invalidPathReservedOnWindows=Invalid path (''{0}'' is reserved on Windows): {1}
+invalidPurgeFactor=Invalid purgeFactor {0}, values have to be in range between 0 and 1
 invalidRedirectLocation=Invalid redirect location {0} -> {1}
 invalidRefAdvertisementLine=Invalid ref advertisement line: ''{1}''
 invalidReflogRevision=Invalid reflog revision: {0}
@@ -577,8 +579,10 @@ pushIsNotSupportedForBundleTransport=Push is not supported for bundle transport
 pushNotPermitted=push not permitted
 pushOptionsNotSupported=Push options not supported; received {0}
 rawLogMessageDoesNotParseAsLogEntry=Raw log message does not parse as log entry
+readConfigFailed=Reading config file ''{0}'' failed
 readerIsRequired=Reader is required
 readingObjectsFromLocalRepositoryFailed=reading objects from local repository failed: {0}
+readLastModifiedFailed=Reading lastModified of {0} failed
 readTimedOut=Read timed out after {0} ms
 receivePackObjectTooLarge1=Object too large, rejecting the pack. Max object size limit is {0} bytes.
 receivePackObjectTooLarge2=Object too large ({0} bytes), rejecting the pack. Max object size limit is {1} bytes.
@@ -701,6 +705,7 @@ theFactoryMustNotBeNull=The factory must not be null
 threadInterruptedWhileRunning="Current thread interrupted while running {0}"
 timeIsUncertain=Time is uncertain
 timerAlreadyTerminated=Timer already terminated
+timeoutMeasureFsTimestampResolution=measuring filesystem timestamp resolution for ''{0}'' timed out, fall back to resolution of 2 seconds
 tooManyCommands=Too many commands
 tooManyFilters=Too many "filter" lines in request
 tooManyIncludeRecursions=Too many recursions; circular includes in config file(s)?

org.eclipse.jgit/src/org/eclipse/jgit/api/AddCommand.java

@@ -50,6 +50,7 @@ import static org.eclipse.jgit.lib.FileMode.TYPE_TREE;
 
 import java.io.IOException;
 import java.io.InputStream;
+import java.time.Instant;
 import java.util.Collection;
 import java.util.LinkedList;
 
@@ -228,7 +229,7 @@ public class AddCommand extends GitCommand<DirCache> {
 
 				if (GITLINK != mode) {
 					entry.setLength(f.getEntryLength());
-					entry.setLastModified(f.getEntryLastModified());
+					entry.setLastModified(f.getEntryLastModifiedInstant());
 					long len = f.getEntryContentLength();
 					// We read and filter the content multiple times.
 					// f.getEntryContentLength() reads and filters the input and
@@ -241,7 +242,7 @@ public class AddCommand extends GitCommand<DirCache> {
 					}
 				} else {
 					entry.setLength(0);
-					entry.setLastModified(0);
+					entry.setLastModified(Instant.ofEpochSecond(0));
 					entry.setObjectId(f.getEntryObjectId());
 				}
 				builder.add(entry);

org.eclipse.jgit/src/org/eclipse/jgit/api/ArchiveCommand.java

@@ -56,13 +56,18 @@ import java.util.concurrent.ConcurrentMap;
 
 import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.JGitInternalException;
+import org.eclipse.jgit.errors.IncorrectObjectTypeException;
 import org.eclipse.jgit.internal.JGitText;
+import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.FileMode;
 import org.eclipse.jgit.lib.MutableObjectId;
 import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.lib.ObjectLoader;
 import org.eclipse.jgit.lib.ObjectReader;
 import org.eclipse.jgit.lib.Repository;
+import org.eclipse.jgit.revwalk.RevCommit;
+import org.eclipse.jgit.revwalk.RevObject;
+import org.eclipse.jgit.revwalk.RevTree;
 import org.eclipse.jgit.revwalk.RevWalk;
 import org.eclipse.jgit.treewalk.TreeWalk;
 import org.eclipse.jgit.treewalk.filter.PathFilterGroup;
@@ -375,13 +380,15 @@ public class ArchiveCommand extends GitCommand<OutputStream> {
 				MutableObjectId idBuf = new MutableObjectId();
 				ObjectReader reader = walk.getObjectReader();
 
-				walk.reset(rw.parseTree(tree));
-				if (!paths.isEmpty())
+				RevObject o = rw.peel(rw.parseAny(tree));
+				walk.reset(getTree(o));
+				if (!paths.isEmpty()) {
 					walk.setFilter(PathFilterGroup.createFromStrings(paths));
+				}
 
 				// Put base directory into archive
 				if (pfx.endsWith("/")) { //$NON-NLS-1$
-					fmt.putEntry(outa, tree, pfx.replaceAll("[/]+$", "/"), //$NON-NLS-1$ //$NON-NLS-2$
+					fmt.putEntry(outa, o, pfx.replaceAll("[/]+$", "/"), //$NON-NLS-1$ //$NON-NLS-2$
 							FileMode.TREE, null);
 				}
 
@@ -392,17 +399,18 @@ public class ArchiveCommand extends GitCommand<OutputStream> {
 					if (walk.isSubtree())
 						walk.enterSubtree();
 
-					if (mode == FileMode.GITLINK)
+					if (mode == FileMode.GITLINK) {
 						// TODO(jrn): Take a callback to recurse
 						// into submodules.
 						mode = FileMode.TREE;
+					}
 
 					if (mode == FileMode.TREE) {
-						fmt.putEntry(outa, tree, name + "/", mode, null); //$NON-NLS-1$
+						fmt.putEntry(outa, o, name + "/", mode, null); //$NON-NLS-1$
 						continue;
 					}
 					walk.getObjectId(idBuf, 0);
-					fmt.putEntry(outa, tree, name, mode, reader.open(idBuf));
+					fmt.putEntry(outa, o, name, mode, reader.open(idBuf));
 				}
 				return out;
 			} finally {
@@ -534,4 +542,19 @@ public class ArchiveCommand extends GitCommand<OutputStream> {
 		this.paths = Arrays.asList(paths);
 		return this;
 	}
+
+	private RevTree getTree(RevObject o)
+			throws IncorrectObjectTypeException {
+		final RevTree t;
+		if (o instanceof RevCommit) {
+			t = ((RevCommit) o).getTree();
+		} else if (!(o instanceof RevTree)) {
+			throw new IncorrectObjectTypeException(tree.toObjectId(),
+					Constants.TYPE_TREE);
+		} else {
+			t = (RevTree) o;
+		}
+		return t;
+	}
+
 }

org.eclipse.jgit/src/org/eclipse/jgit/api/CherryPickCommand.java

@@ -157,8 +157,8 @@ public class CherryPickCommand extends GitCommand<CherryPickResult> {
 				merger.setCommitNames(new String[] { "BASE", ourName, //$NON-NLS-1$
 						cherryPickName });
 				if (merger.merge(newHead, srcCommit)) {
-					if (AnyObjectId.equals(newHead.getTree().getId(), merger
-							.getResultTreeId()))
+					if (AnyObjectId.isEqual(newHead.getTree().getId(),
+							merger.getResultTreeId()))
 						continue;
 					DirCacheCheckout dco = new DirCacheCheckout(repo,
 							newHead.getTree(), repo.lockDirCache(),

org.eclipse.jgit/src/org/eclipse/jgit/api/CommitCommand.java

@@ -413,7 +413,7 @@ public class CommitCommand extends GitCommand<RevCommit> {
 						final DirCacheEntry dcEntry = new DirCacheEntry(path);
 						long entryLength = fTree.getEntryLength();
 						dcEntry.setLength(entryLength);
-						dcEntry.setLastModified(fTree.getEntryLastModified());
+						dcEntry.setLastModified(fTree.getEntryLastModifiedInstant());
 						dcEntry.setFileMode(fTree.getIndexFileMode(dcTree));
 
 						boolean objectExists = (dcTree != null

org.eclipse.jgit/src/org/eclipse/jgit/api/RebaseCommand.java

@@ -575,7 +575,7 @@ public class RebaseCommand extends GitCommand<RebaseResult> {
 			ObjectId headId = getHead().getObjectId();
 			// getHead() checks for null
 			assert headId != null;
-			if (!AnyObjectId.equals(headId, newParents.get(0)))
+			if (!AnyObjectId.isEqual(headId, newParents.get(0)))
 				checkoutCommit(headId.getName(), newParents.get(0));
 
 			// Use the cherry-pick strategy if all non-first parents did not

org.eclipse.jgit/src/org/eclipse/jgit/api/ResetCommand.java

@@ -422,7 +422,7 @@ public class ResetCommand extends GitCommand<Ref> {
 						DirCacheIterator.class);
 				if (dcIter != null && dcIter.idEqual(cIter)) {
 					DirCacheEntry indexEntry = dcIter.getDirCacheEntry();
-					entry.setLastModified(indexEntry.getLastModified());
+					entry.setLastModified(indexEntry.getLastModifiedInstant());
 					entry.setLength(indexEntry.getLength());
 				}
 

org.eclipse.jgit/src/org/eclipse/jgit/api/RevertCommand.java

@@ -175,8 +175,8 @@ public class RevertCommand extends GitCommand<RevCommit> {
 						+ "This reverts commit " + srcCommit.getId().getName() //$NON-NLS-1$
 						+ ".\n"; //$NON-NLS-1$
 				if (merger.merge(headCommit, srcParent)) {
-					if (AnyObjectId.equals(headCommit.getTree().getId(), merger
-							.getResultTreeId()))
+					if (AnyObjectId.isEqual(headCommit.getTree().getId(),
+							merger.getResultTreeId()))
 						continue;
 					DirCacheCheckout dco = new DirCacheCheckout(repo,
 							headCommit.getTree(), repo.lockDirCache(),

org.eclipse.jgit/src/org/eclipse/jgit/api/StashApplyCommand.java

@@ -362,7 +362,7 @@ public class StashApplyCommand extends GitCommand<ObjectId> {
 						DirCacheIterator.class);
 				if (dcIter != null && dcIter.idEqual(cIter)) {
 					DirCacheEntry indexEntry = dcIter.getDirCacheEntry();
-					entry.setLastModified(indexEntry.getLastModified());
+					entry.setLastModified(indexEntry.getLastModifiedInstant());
 					entry.setLength(indexEntry.getLength());
 				}
 

org.eclipse.jgit/src/org/eclipse/jgit/api/StashCreateCommand.java

@@ -300,7 +300,8 @@ public class StashCreateCommand extends GitCommand<RevCommit> {
 						final DirCacheEntry entry = new DirCacheEntry(
 								treeWalk.getRawPath());
 						entry.setLength(wtIter.getEntryLength());
-						entry.setLastModified(wtIter.getEntryLastModified());
+						entry.setLastModified(
+								wtIter.getEntryLastModifiedInstant());
 						entry.setFileMode(wtIter.getEntryFileMode());
 						long contentLength = wtIter.getEntryContentLength();
 						try (InputStream in = wtIter.openEntryStream()) {

org.eclipse.jgit/src/org/eclipse/jgit/dircache/DirCache.java

@@ -58,6 +58,7 @@ import java.io.OutputStream;
 import java.security.DigestOutputStream;
 import java.security.MessageDigest;
 import java.text.MessageFormat;
+import java.time.Instant;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Comparator;
@@ -489,8 +490,7 @@ public class DirCache {
 			throw new CorruptObjectException(JGitText.get().DIRCHasTooManyEntries);
 
 		snapshot = FileSnapshot.save(liveFile);
-		int smudge_s = (int) (snapshot.lastModified() / 1000);
-		int smudge_ns = ((int) (snapshot.lastModified() % 1000)) * 1000000;
+		Instant smudge = snapshot.lastModifiedInstant();
 
 		// Load the individual file entries.
 		//
@@ -499,8 +499,9 @@ public class DirCache {
 		sortedEntries = new DirCacheEntry[entryCnt];
 
 		final MutableInteger infoAt = new MutableInteger();
-		for (int i = 0; i < entryCnt; i++)
-			sortedEntries[i] = new DirCacheEntry(infos, infoAt, in, md, smudge_s, smudge_ns);
+		for (int i = 0; i < entryCnt; i++) {
+			sortedEntries[i] = new DirCacheEntry(infos, infoAt, in, md, smudge);
+		}
 
 		// After the file entries are index extensions, and then a footer.
 		//
@@ -665,8 +666,8 @@ public class DirCache {
 			// so we use the current timestamp as a approximation.
 			myLock.createCommitSnapshot();
 			snapshot = myLock.getCommitSnapshot();
-			smudge_s = (int) (snapshot.lastModified() / 1000);
-			smudge_ns = ((int) (snapshot.lastModified() % 1000)) * 1000000;
+			smudge_s = (int) (snapshot.lastModifiedInstant().getEpochSecond());
+			smudge_ns = snapshot.lastModifiedInstant().getNano();
 		} else {
 			// Used in unit tests only
 			smudge_ns = 0;
@@ -1011,7 +1012,7 @@ public class DirCache {
 				DirCacheEntry entry = iIter.getDirCacheEntry();
 				if (entry.isSmudged() && iIter.idEqual(fIter)) {
 					entry.setLength(fIter.getEntryLength());
-					entry.setLastModified(fIter.getEntryLastModified());
+					entry.setLastModified(fIter.getEntryLastModifiedInstant());
 				}
 			}
 		}

org.eclipse.jgit/src/org/eclipse/jgit/dircache/DirCacheCheckout.java

@@ -50,6 +50,7 @@ import java.io.IOException;
 import java.io.OutputStream;
 import java.nio.file.StandardCopyOption;
 import java.text.MessageFormat;
+import java.time.Instant;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.Iterator;
@@ -427,8 +428,10 @@ public class DirCacheCheckout {
 					// update the timestamp of the index with the one from the
 					// file if not set, as we are sure to be in sync here.
 					DirCacheEntry entry = i.getDirCacheEntry();
-					if (entry.getLastModified() == 0)
-						entry.setLastModified(f.getEntryLastModified());
+					Instant mtime = entry.getLastModifiedInstant();
+					if (mtime == null || mtime.equals(Instant.EPOCH)) {
+						entry.setLastModified(f.getEntryLastModifiedInstant());
+					}
 					keep(entry, f);
 				}
 			} else
@@ -640,7 +643,7 @@ public class DirCacheCheckout {
 		File gitlinkDir = new File(repo.getWorkTree(), path);
 		FileUtils.mkdirs(gitlinkDir, true);
 		FS fs = repo.getFS();
-		entry.setLastModified(fs.lastModified(gitlinkDir));
+		entry.setLastModified(fs.lastModifiedInstant(gitlinkDir));
 	}
 
 	private static ArrayList<String> filterOut(ArrayList<String> strings,
@@ -1477,7 +1480,7 @@ public class DirCacheCheckout {
 			}
 			fs.createSymLink(f, target);
 			entry.setLength(bytes.length);
-			entry.setLastModified(fs.lastModified(f));
+			entry.setLastModified(fs.lastModifiedInstant(f));
 			return;
 		}
 
@@ -1546,7 +1549,7 @@ public class DirCacheCheckout {
 				FileUtils.delete(tmpFile);
 			}
 		}
-		entry.setLastModified(fs.lastModified(f));
+		entry.setLastModified(fs.lastModifiedInstant(f));
 	}
 
 	// Run an external filter command

org.eclipse.jgit/src/org/eclipse/jgit/dircache/DirCacheEntry.java

@@ -56,6 +56,7 @@ import java.io.OutputStream;
 import java.nio.ByteBuffer;
 import java.security.MessageDigest;
 import java.text.MessageFormat;
+import java.time.Instant;
 import java.util.Arrays;
 
 import org.eclipse.jgit.errors.CorruptObjectException;
@@ -145,8 +146,8 @@ public class DirCacheEntry {
 	private byte inCoreFlags;
 
 	DirCacheEntry(final byte[] sharedInfo, final MutableInteger infoAt,
-			final InputStream in, final MessageDigest md, final int smudge_s,
-			final int smudge_ns) throws IOException {
+			final InputStream in, final MessageDigest md, final Instant smudge)
+			throws IOException {
 		info = sharedInfo;
 		infoOffset = infoAt.value;
 
@@ -215,8 +216,9 @@ public class DirCacheEntry {
 			md.update(nullpad, 0, padLen);
 		}
 
-		if (mightBeRacilyClean(smudge_s, smudge_ns))
+		if (mightBeRacilyClean(smudge)) {
 			smudgeRacilyClean();
+		}
 	}
 
 	/**
@@ -344,8 +346,29 @@ public class DirCacheEntry {
 	 * @param smudge_ns
 	 *            nanoseconds component of the index's last modified time.
 	 * @return true if extra careful checks should be used.
+	 * @deprecated use {@link #mightBeRacilyClean(Instant)} instead
 	 */
+	@Deprecated
 	public final boolean mightBeRacilyClean(int smudge_s, int smudge_ns) {
+		return mightBeRacilyClean(Instant.ofEpochSecond(smudge_s, smudge_ns));
+	}
+
+	/**
+	 * Is it possible for this entry to be accidentally assumed clean?
+	 * <p>
+	 * The "racy git" problem happens when a work file can be updated faster
+	 * than the filesystem records file modification timestamps. It is possible
+	 * for an application to edit a work file, update the index, then edit it
+	 * again before the filesystem will give the work file a new modification
+	 * timestamp. This method tests to see if file was written out at the same
+	 * time as the index.
+	 *
+	 * @param smudge
+	 *            index's last modified time.
+	 * @return true if extra careful checks should be used.
+	 * @since 5.1.9
+	 */
+	public final boolean mightBeRacilyClean(Instant smudge) {
 		// If the index has a modification time then it came from disk
 		// and was not generated from scratch in memory. In such cases
 		// the entry is 'racily clean' if the entry's cached modification
@@ -355,8 +378,9 @@ public class DirCacheEntry {
 		//
 		final int base = infoOffset + P_MTIME;
 		final int mtime = NB.decodeInt32(info, base);
-		if (smudge_s == mtime)
-			return smudge_ns <= NB.decodeInt32(info, base + 4);
+		if (smudge.getEpochSecond() == mtime) {
+			return smudge.getNano() <= NB.decodeInt32(info, base + 4);
+		}
 		return false;
 	}
 
@@ -424,9 +448,9 @@ public class DirCacheEntry {
 	 */
 	public void setAssumeValid(boolean assume) {
 		if (assume)
-			info[infoOffset + P_FLAGS] |= ASSUME_VALID;
+			info[infoOffset + P_FLAGS] |= (byte) ASSUME_VALID;
 		else
-			info[infoOffset + P_FLAGS] &= ~ASSUME_VALID;
+			info[infoOffset + P_FLAGS] &= (byte) ~ASSUME_VALID;
 	}
 
 	/**
@@ -446,9 +470,9 @@ public class DirCacheEntry {
 	 */
 	public void setUpdateNeeded(boolean updateNeeded) {
 		if (updateNeeded)
-			inCoreFlags |= UPDATE_NEEDED;
+			inCoreFlags |= (byte) UPDATE_NEEDED;
 		else
-			inCoreFlags &= ~UPDATE_NEEDED;
+			inCoreFlags &= (byte) ~UPDATE_NEEDED;
 	}
 
 	/**
@@ -563,21 +587,50 @@ public class DirCacheEntry {
 	 *
 	 * @return last modification time of this file, in milliseconds since the
 	 *         Java epoch (midnight Jan 1, 1970 UTC).
+	 * @deprecated use {@link #getLastModifiedInstant()} instead
 	 */
+	@Deprecated
 	public long getLastModified() {
 		return decodeTS(P_MTIME);
 	}
 
+	/**
+	 * Get the cached last modification date of this file.
+	 * <p>
+	 * One of the indicators that the file has been modified by an application
+	 * changing the working tree is if the last modification time for the file
+	 * differs from the time stored in this entry.
+	 *
+	 * @return last modification time of this file.
+	 * @since 5.1.9
+	 */
+	public Instant getLastModifiedInstant() {
+		return decodeTSInstant(P_MTIME);
+	}
+
 	/**
 	 * Set the cached last modification date of this file, using milliseconds.
 	 *
 	 * @param when
 	 *            new cached modification date of the file, in milliseconds.
+	 * @deprecated use {@link #setLastModified(Instant)} instead
 	 */
+	@Deprecated
 	public void setLastModified(long when) {
 		encodeTS(P_MTIME, when);
 	}
 
+	/**
+	 * Set the cached last modification date of this file.
+	 *
+	 * @param when
+	 *            new cached modification date of the file.
+	 * @since 5.1.9
+	 */
+	public void setLastModified(Instant when) {
+		encodeTS(P_MTIME, when);
+	}
+
 	/**
 	 * Get the cached size (mod 4 GB) (in bytes) of this file.
 	 * <p>
@@ -692,7 +745,8 @@ public class DirCacheEntry {
 	@SuppressWarnings("nls")
 	@Override
 	public String toString() {
-		return getFileMode() + " " + getLength() + " " + getLastModified()
+		return getFileMode() + " " + getLength() + " "
+				+ getLastModifiedInstant()
 				+ " " + getObjectId() + " " + getStage() + " "
 				+ getPathString() + "\n";
 	}
@@ -750,12 +804,25 @@ public class DirCacheEntry {
 		return 1000L * sec + ms;
 	}
 
+	private Instant decodeTSInstant(int pIdx) {
+		final int base = infoOffset + pIdx;
+		final int sec = NB.decodeInt32(info, base);
+		final int nano = NB.decodeInt32(info, base + 4);
+		return Instant.ofEpochSecond(sec, nano);
+	}
+
 	private void encodeTS(int pIdx, long when) {
 		final int base = infoOffset + pIdx;
 		NB.encodeInt32(info, base, (int) (when / 1000));
 		NB.encodeInt32(info, base + 4, ((int) (when % 1000)) * 1000000);
 	}
 
+	private void encodeTS(int pIdx, Instant when) {
+		final int base = infoOffset + pIdx;
+		NB.encodeInt32(info, base, (int) when.getEpochSecond());
+		NB.encodeInt32(info, base + 4, when.getNano());
+	}
+
 	private int getExtendedFlags() {
 		if (isExtended())
 			return NB.decodeUInt16(info, infoOffset + P_FLAGS2) << 16;

org.eclipse.jgit/src/org/eclipse/jgit/errors/IncorrectObjectTypeException.java

@@ -63,7 +63,7 @@ public class IncorrectObjectTypeException extends IOException {
 	private static final long serialVersionUID = 1L;
 
 	/**
-	 * Construct and IncorrectObjectTypeException for the specified object id.
+	 * Construct an IncorrectObjectTypeException for the specified object id.
 	 *
 	 * Provide the type to make it easier to track down the problem.
 	 *
@@ -75,7 +75,7 @@ public class IncorrectObjectTypeException extends IOException {
 	}
 
 	/**
-	 * Construct and IncorrectObjectTypeException for the specified object id.
+	 * Construct an IncorrectObjectTypeException for the specified object id.
 	 *
 	 * Provide the type to make it easier to track down the problem.
 	 *

org.eclipse.jgit/src/org/eclipse/jgit/internal/JGitText.java

@@ -166,6 +166,7 @@ public class JGitText extends TranslationBundle {
 	/***/ public String cannotReadTree;
 	/***/ public String cannotRebaseWithoutCurrentHead;
 	/***/ public String cannotResolveLocalTrackingRefForUpdating;
+	/***/ public String cannotSaveConfig;
 	/***/ public String cannotSquashFixupWithoutPreviousCommit;
 	/***/ public String cannotStoreObjects;
 	/***/ public String cannotResolveUniquelyAbbrevObjectId;
@@ -467,6 +468,7 @@ public class JGitText extends TranslationBundle {
 	/***/ public String invalidPathPeriodAtEndWindows;
 	/***/ public String invalidPathSpaceAtEndWindows;
 	/***/ public String invalidPathReservedOnWindows;
+	/***/ public String invalidPurgeFactor;
 	/***/ public String invalidRedirectLocation;
 	/***/ public String invalidRefAdvertisementLine;
 	/***/ public String invalidReflogRevision;
@@ -638,8 +640,10 @@ public class JGitText extends TranslationBundle {
 	/***/ public String pushNotPermitted;
 	/***/ public String pushOptionsNotSupported;
 	/***/ public String rawLogMessageDoesNotParseAsLogEntry;
+	/***/ public String readConfigFailed;
 	/***/ public String readerIsRequired;
 	/***/ public String readingObjectsFromLocalRepositoryFailed;
+	/***/ public String readLastModifiedFailed;
 	/***/ public String readTimedOut;
 	/***/ public String receivePackObjectTooLarge1;
 	/***/ public String receivePackObjectTooLarge2;
@@ -757,6 +761,7 @@ public class JGitText extends TranslationBundle {
 	/***/ public String tagAlreadyExists;
 	/***/ public String tagNameInvalid;
 	/***/ public String tagOnRepoWithoutHEADCurrentlyNotSupported;
+	/***/ public String timeoutMeasureFsTimestampResolution;
 	/***/ public String transactionAborted;
 	/***/ public String theFactoryMustNotBeNull;
 	/***/ public String threadInterruptedWhileRunning;

org.eclipse.jgit/src/org/eclipse/jgit/internal/ketch/KetchReplica.java

@@ -345,7 +345,7 @@ public abstract class KetchReplica {
 	}
 
 	private static boolean equals(@Nullable ObjectId a, LogIndex b) {
-		return a != null && b != null && AnyObjectId.equals(a, b);
+		return a != null && b != null && AnyObjectId.isEqual(a, b);
 	}
 
 	/**
@@ -749,7 +749,7 @@ public abstract class KetchReplica {
 				Ref oldRef = remote.remove(name);
 				ObjectId oldId = getId(oldRef);
 				ObjectId newId = tw.getObjectId(0);
-				if (!AnyObjectId.equals(oldId, newId)) {
+				if (!AnyObjectId.isEqual(oldId, newId)) {
 					delta.add(new ReceiveCommand(oldId, newId, name));
 				}
 			}

org.eclipse.jgit/src/org/eclipse/jgit/internal/ketch/LagCheck.java

@@ -106,7 +106,7 @@ class LagCheck implements AutoCloseable {
 			return UNKNOWN;
 		}
 
-		if (AnyObjectId.equals(remoteId, ObjectId.zeroId())) {
+		if (AnyObjectId.isEqual(remoteId, ObjectId.zeroId())) {
 			// Replica does not have the txnAccepted reference.
 			return LAGGING;
 		}

org.eclipse.jgit/src/org/eclipse/jgit/internal/ketch/RemoteGitReplica.java

@@ -200,7 +200,7 @@ public class RemoteGitReplica extends KetchReplica {
 	private static boolean isExpectedValue(Map<String, Ref> adv,
 			RemoteRefUpdate u) {
 		Ref r = adv.get(u.getRemoteName());
-		if (!AnyObjectId.equals(getId(r), u.getExpectedOldObjectId())) {
+		if (!AnyObjectId.isEqual(getId(r), u.getExpectedOldObjectId())) {
 			((RemoteCommand) u).cmd.setResult(LOCK_FAILURE);
 			return false;
 		}

org.eclipse.jgit/src/org/eclipse/jgit/internal/ketch/StageBuilder.java

@@ -138,7 +138,7 @@ public class StageBuilder {
 		try (RevWalk rw = new RevWalk(git);
 				TreeWalk tw = new TreeWalk(rw.getObjectReader());
 				ObjectInserter ins = git.newObjectInserter()) {
-			if (AnyObjectId.equals(oldTree, ObjectId.zeroId())) {
+			if (AnyObjectId.isEqual(oldTree, ObjectId.zeroId())) {
 				tw.addTree(new EmptyTreeIterator());
 			} else {
 				tw.addTree(rw.parseTree(oldTree));

org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsGarbageCollector.java

@@ -661,7 +661,7 @@ public class DfsGarbageCollector {
 	private int objectsBefore() {
 		int cnt = 0;
 		for (DfsPackFile p : packsBefore)
-			cnt += p.getPackDescription().getObjectCount();
+			cnt += (int) p.getPackDescription().getObjectCount();
 		return cnt;
 	}
 

org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsPackParser.java

@@ -432,7 +432,7 @@ public class DfsPackParser extends PackParser {
 		buf[len++] = (byte) ((typeCode << 4) | (sz & 15));
 		sz >>>= 4;
 		while (sz > 0) {
-			buf[len - 1] |= 0x80;
+			buf[len - 1] |= (byte) 0x80;
 			buf[len++] = (byte) (sz & 0x7f);
 			sz >>>= 7;
 		}

org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/ReftableBatchRefUpdate.java

@@ -252,7 +252,7 @@ public class ReftableBatchRefUpdate extends BatchRefUpdate {
 
 	private static boolean matchOld(ReceiveCommand cmd, @Nullable Ref ref) {
 		if (ref == null) {
-			return AnyObjectId.equals(ObjectId.zeroId(), cmd.getOldId())
+			return AnyObjectId.isEqual(ObjectId.zeroId(), cmd.getOldId())
 					&& cmd.getOldSymref() == null;
 		} else if (ref.isSymbolic()) {
 			return ref.getTarget().getName().equals(cmd.getOldSymref());
@@ -368,7 +368,7 @@ public class ReftableBatchRefUpdate extends BatchRefUpdate {
 			String name = cmd.getRefName();
 			ObjectId newId = cmd.getNewId();
 			String newSymref = cmd.getNewSymref();
-			if (AnyObjectId.equals(ObjectId.zeroId(), newId)
+			if (AnyObjectId.isEqual(ObjectId.zeroId(), newId)
 					&& newSymref == null) {
 				refs.add(new ObjectIdRef.Unpeeled(NEW, name, null));
 				continue;

org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/FileSnapshot.java

@@ -43,19 +43,24 @@
 
 package org.eclipse.jgit.internal.storage.file;
 
+import static org.eclipse.jgit.util.FS.FileStoreAttributes.FALLBACK_FILESTORE_ATTRIBUTES;
+import static org.eclipse.jgit.util.FS.FileStoreAttributes.FALLBACK_TIMESTAMP_RESOLUTION;
 import java.io.File;
 import java.io.IOException;
 import java.nio.file.attribute.BasicFileAttributes;
-import java.text.DateFormat;
-import java.text.SimpleDateFormat;
 import java.time.Duration;
-import java.util.Date;
+import java.time.Instant;
+import java.time.ZoneId;
+import java.time.format.DateTimeFormatter;
 import java.util.Locale;
 import java.util.Objects;
 import java.util.concurrent.TimeUnit;
 
 import org.eclipse.jgit.annotations.NonNull;
 import org.eclipse.jgit.util.FS;
+import org.eclipse.jgit.util.FS.FileStoreAttributes;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 /**
  * Caches when a file was last read, making it possible to detect future edits.
@@ -74,6 +79,8 @@ import org.eclipse.jgit.util.FS;
  * file is less than 3 seconds ago.
  */
 public class FileSnapshot {
+	private static final Logger LOG = LoggerFactory
+			.getLogger(FileSnapshot.class);
 	/**
 	 * An unknown file size.
 	 *
@@ -81,8 +88,14 @@ public class FileSnapshot {
 	 */
 	public static final long UNKNOWN_SIZE = -1;
 
+	private static final Instant UNKNOWN_TIME = Instant.ofEpochMilli(-1);
+
 	private static final Object MISSING_FILEKEY = new Object();
 
+	private static final DateTimeFormatter dateFmt = DateTimeFormatter
+			.ofPattern("yyyy-MM-dd HH:mm:ss.nnnnnnnnn") //$NON-NLS-1$
+			.withLocale(Locale.getDefault()).withZone(ZoneId.systemDefault());
+
 	/**
 	 * A FileSnapshot that is considered to always be modified.
 	 * <p>
@@ -90,8 +103,8 @@ public class FileSnapshot {
 	 * file, but only after {@link #isModified(File)} gets invoked. The returned
 	 * snapshot contains only invalid status information.
 	 */
-	public static final FileSnapshot DIRTY = new FileSnapshot(-1, -1,
-			UNKNOWN_SIZE, Duration.ZERO, MISSING_FILEKEY);
+	public static final FileSnapshot DIRTY = new FileSnapshot(UNKNOWN_TIME,
+			UNKNOWN_TIME, UNKNOWN_SIZE, Duration.ZERO, MISSING_FILEKEY);
 
 	/**
 	 * A FileSnapshot that is clean if the file does not exist.
@@ -100,8 +113,8 @@ public class FileSnapshot {
 	 * file to be clean. {@link #isModified(File)} will return false if the file
 	 * path does not exist.
 	 */
-	public static final FileSnapshot MISSING_FILE = new FileSnapshot(0, 0, 0,
-			Duration.ZERO, MISSING_FILEKEY) {
+	public static final FileSnapshot MISSING_FILE = new FileSnapshot(
+			Instant.EPOCH, Instant.EPOCH, 0, Duration.ZERO, MISSING_FILEKEY) {
 		@Override
 		public boolean isModified(File path) {
 			return FS.DETECTED.exists(path);
@@ -122,6 +135,22 @@ public class FileSnapshot {
 		return new FileSnapshot(path);
 	}
 
+	/**
+	 * Record a snapshot for a specific file path without using config file to
+	 * get filesystem timestamp resolution.
+	 * <p>
+	 * This method should be invoked before the file is accessed. It is used by
+	 * FileBasedConfig to avoid endless recursion.
+	 *
+	 * @param path
+	 *            the path to later remember. The path's current status
+	 *            information is saved.
+	 * @return the snapshot.
+	 */
+	public static FileSnapshot saveNoConfig(File path) {
+		return new FileSnapshot(path, false);
+	}
+
 	private static Object getFileKey(BasicFileAttributes fileAttributes) {
 		Object fileKey = fileAttributes.fileKey();
 		return fileKey == null ? MISSING_FILEKEY : fileKey;
@@ -141,18 +170,41 @@ public class FileSnapshot {
 	 * @param modified
 	 *            the last modification time of the file
 	 * @return the snapshot.
+	 * @deprecated use {@link #save(Instant)} instead.
 	 */
+	@Deprecated
 	public static FileSnapshot save(long modified) {
-		final long read = System.currentTimeMillis();
-		return new FileSnapshot(read, modified, -1, Duration.ZERO,
-				MISSING_FILEKEY);
+		final Instant read = Instant.now();
+		return new FileSnapshot(read, Instant.ofEpochMilli(modified),
+				UNKNOWN_SIZE, FALLBACK_TIMESTAMP_RESOLUTION, MISSING_FILEKEY);
+	}
+
+	/**
+	 * Record a snapshot for a file for which the last modification time is
+	 * already known.
+	 * <p>
+	 * This method should be invoked before the file is accessed.
+	 * <p>
+	 * Note that this method cannot rely on measuring file timestamp resolution
+	 * to avoid racy git issues caused by finite file timestamp resolution since
+	 * it's unknown in which filesystem the file is located. Hence the worst
+	 * case fallback for timestamp resolution is used.
+	 *
+	 * @param modified
+	 *            the last modification time of the file
+	 * @return the snapshot.
+	 */
+	public static FileSnapshot save(Instant modified) {
+		final Instant read = Instant.now();
+		return new FileSnapshot(read, modified, UNKNOWN_SIZE,
+				FALLBACK_TIMESTAMP_RESOLUTION, MISSING_FILEKEY);
 	}
 
 	/** Last observed modification time of the path. */
-	private final long lastModified;
+	private final Instant lastModified;
 
 	/** Last wall-clock time the path was read. */
-	private volatile long lastRead;
+	private volatile Instant lastRead;
 
 	/** True once {@link #lastRead} is far later than {@link #lastModified}. */
 	private boolean cannotBeRacilyClean;
@@ -162,8 +214,8 @@ public class FileSnapshot {
 	 * When set to {@link #UNKNOWN_SIZE} the size is not considered for modification checks. */
 	private final long size;
 
-	/** measured filesystem timestamp resolution */
-	private Duration fsTimestampResolution;
+	/** measured FileStore attributes */
+	private FileStoreAttributes fileStoreAttributeCache;
 
 	/**
 	 * Object that uniquely identifies the given file, or {@code
@@ -171,31 +223,57 @@ public class FileSnapshot {
 	 */
 	private final Object fileKey;
 
+	private final File file;
+
 	/**
 	 * Record a snapshot for a specific file path.
 	 * <p>
 	 * This method should be invoked before the file is accessed.
 	 *
-	 * @param path
-	 *            the path to later remember. The path's current status
+	 * @param file
+	 *            the path to remember meta data for. The path's current status
 	 *            information is saved.
 	 */
-	protected FileSnapshot(File path) {
-		this.lastRead = System.currentTimeMillis();
-		this.fsTimestampResolution = FS
-				.getFsTimerResolution(path.toPath().getParent());
+	protected FileSnapshot(File file) {
+		this(file, true);
+	}
+
+	/**
+	 * Record a snapshot for a specific file path.
+	 * <p>
+	 * This method should be invoked before the file is accessed.
+	 *
+	 * @param file
+	 *            the path to remember meta data for. The path's current status
+	 *            information is saved.
+	 * @param useConfig
+	 *            if {@code true} read filesystem time resolution from
+	 *            configuration file otherwise use fallback resolution
+	 */
+	protected FileSnapshot(File file, boolean useConfig) {
+		this.file = file;
+		this.lastRead = Instant.now();
+		this.fileStoreAttributeCache = useConfig
+				? FS.getFileStoreAttributes(file.toPath().getParent())
+				: FALLBACK_FILESTORE_ATTRIBUTES;
 		BasicFileAttributes fileAttributes = null;
 		try {
-			fileAttributes = FS.DETECTED.fileAttributes(path);
+			fileAttributes = FS.DETECTED.fileAttributes(file);
 		} catch (IOException e) {
-			this.lastModified = path.lastModified();
-			this.size = path.length();
+			this.lastModified = Instant.ofEpochMilli(file.lastModified());
+			this.size = file.length();
 			this.fileKey = MISSING_FILEKEY;
 			return;
 		}
-		this.lastModified = fileAttributes.lastModifiedTime().toMillis();
+		this.lastModified = fileAttributes.lastModifiedTime().toInstant();
 		this.size = fileAttributes.size();
 		this.fileKey = getFileKey(fileAttributes);
+		if (LOG.isDebugEnabled()) {
+			LOG.debug("file={}, create new FileSnapshot: lastRead={}, lastModified={}, size={}, fileKey={}", //$NON-NLS-1$
+					file, dateFmt.format(lastRead),
+					dateFmt.format(lastModified), Long.valueOf(size),
+					fileKey.toString());
+		}
 	}
 
 	private boolean sizeChanged;
@@ -206,11 +284,17 @@ public class FileSnapshot {
 
 	private boolean wasRacyClean;
 
-	private FileSnapshot(long read, long modified, long size,
+	private long delta;
+
+	private long racyThreshold;
+
+	private FileSnapshot(Instant read, Instant modified, long size,
 			@NonNull Duration fsTimestampResolution, @NonNull Object fileKey) {
+		this.file = null;
 		this.lastRead = read;
 		this.lastModified = modified;
-		this.fsTimestampResolution = fsTimestampResolution;
+		this.fileStoreAttributeCache = new FileStoreAttributes(
+				fsTimestampResolution);
 		this.size = size;
 		this.fileKey = fileKey;
 	}
@@ -219,8 +303,19 @@ public class FileSnapshot {
 	 * Get time of last snapshot update
 	 *
 	 * @return time of last snapshot update
+	 * @deprecated use {@link #lastModifiedInstant()} instead
 	 */
+	@Deprecated
 	public long lastModified() {
+		return lastModified.toEpochMilli();
+	}
+
+	/**
+	 * Get time of last snapshot update
+	 *
+	 * @return time of last snapshot update
+	 */
+	public Instant lastModifiedInstant() {
 		return lastModified;
 	}
 
@@ -239,16 +334,16 @@ public class FileSnapshot {
 	 * @return true if the path needs to be read again.
 	 */
 	public boolean isModified(File path) {
-		long currLastModified;
+		Instant currLastModified;
 		long currSize;
 		Object currFileKey;
 		try {
 			BasicFileAttributes fileAttributes = FS.DETECTED.fileAttributes(path);
-			currLastModified = fileAttributes.lastModifiedTime().toMillis();
+			currLastModified = fileAttributes.lastModifiedTime().toInstant();
 			currSize = fileAttributes.size();
 			currFileKey = getFileKey(fileAttributes);
 		} catch (IOException e) {
-			currLastModified = path.lastModified();
+			currLastModified = Instant.ofEpochMilli(path.lastModified());
 			currSize = path.length();
 			currFileKey = MISSING_FILEKEY;
 		}
@@ -290,7 +385,7 @@ public class FileSnapshot {
 	 *            the other snapshot.
 	 */
 	public void setClean(FileSnapshot other) {
-		final long now = other.lastRead;
+		final Instant now = other.lastRead;
 		if (!isRacyClean(now)) {
 			cannotBeRacilyClean = true;
 		}
@@ -304,9 +399,10 @@ public class FileSnapshot {
 	 *             if sleep was interrupted
 	 */
 	public void waitUntilNotRacy() throws InterruptedException {
-		while (isRacyClean(System.currentTimeMillis())) {
-			TimeUnit.NANOSECONDS
-					.sleep((fsTimestampResolution.toNanos() + 1) * 11 / 10);
+		long timestampResolution = fileStoreAttributeCache
+				.getFsTimestampResolution().toNanos();
+		while (isRacyClean(Instant.now())) {
+			TimeUnit.NANOSECONDS.sleep(timestampResolution);
 		}
 	}
 
@@ -317,8 +413,10 @@ public class FileSnapshot {
 	 *            the other snapshot.
 	 * @return true if the two snapshots share the same information.
 	 */
+	@SuppressWarnings("NonOverridingEquals")
 	public boolean equals(FileSnapshot other) {
-		return lastModified == other.lastModified && size == other.size
+		boolean sizeEq = size == UNKNOWN_SIZE || other.size == UNKNOWN_SIZE || size == other.size;
+		return lastModified.equals(other.lastModified) && sizeEq
 				&& Objects.equals(fileKey, other.fileKey);
 	}
 
@@ -341,8 +439,7 @@ public class FileSnapshot {
 	/** {@inheritDoc} */
 	@Override
 	public int hashCode() {
-		return Objects.hash(Long.valueOf(lastModified), Long.valueOf(size),
-				fileKey);
+		return Objects.hash(lastModified, Long.valueOf(size), fileKey);
 	}
 
 	/**
@@ -377,8 +474,24 @@ public class FileSnapshot {
 		return wasRacyClean;
 	}
 
+	/**
+	 * @return the delta in nanoseconds between lastModified and lastRead during
+	 *         last racy check
+	 */
+	public long lastDelta() {
+		return delta;
+	}
+
+	/**
+	 * @return the racyLimitNanos threshold in nanoseconds during last racy
+	 *         check
+	 */
+	public long lastRacyThreshold() {
+		return racyThreshold;
+	}
+
 	/** {@inheritDoc} */
-	@SuppressWarnings("nls")
+	@SuppressWarnings({ "nls", "ReferenceEquality" })
 	@Override
 	public String toString() {
 		if (this == DIRTY) {
@@ -387,24 +500,46 @@ public class FileSnapshot {
 		if (this == MISSING_FILE) {
 			return "MISSING_FILE";
 		}
-		DateFormat f = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss.SSS",
-				Locale.US);
-		return "FileSnapshot[modified: " + f.format(new Date(lastModified))
-				+ ", read: " + f.format(new Date(lastRead)) + ", size:" + size
+		return "FileSnapshot[modified: " + dateFmt.format(lastModified)
+				+ ", read: " + dateFmt.format(lastRead) + ", size:" + size
 				+ ", fileKey: " + fileKey + "]";
 	}
 
-	private boolean isRacyClean(long read) {
-		// add a 10% safety margin
-		long racyNanos = (fsTimestampResolution.toNanos() + 1) * 11 / 10;
-		return wasRacyClean = (read - lastModified) * 1_000_000 <= racyNanos;
+	private boolean isRacyClean(Instant read) {
+		racyThreshold = getEffectiveRacyThreshold();
+		delta = Duration.between(lastModified, read).toNanos();
+		wasRacyClean = delta <= racyThreshold;
+		if (LOG.isDebugEnabled()) {
+			LOG.debug(
+					"file={}, isRacyClean={}, read={}, lastModified={}, delta={} ns, racy<={} ns", //$NON-NLS-1$
+					file, Boolean.valueOf(wasRacyClean), dateFmt.format(read),
+					dateFmt.format(lastModified), Long.valueOf(delta),
+					Long.valueOf(racyThreshold));
+		}
+		return wasRacyClean;
+	}
+
+	private long getEffectiveRacyThreshold() {
+		long timestampResolution = fileStoreAttributeCache
+				.getFsTimestampResolution().toNanos();
+		long minRacyInterval = fileStoreAttributeCache.getMinimalRacyInterval()
+				.toNanos();
+		long max = Math.max(timestampResolution, minRacyInterval);
+		// safety margin: factor 2.5 below 100ms otherwise 1.25
+		return max < 100_000_000L ? max * 5 / 2 : max * 5 / 4;
 	}
 
-	private boolean isModified(long currLastModified) {
+	private boolean isModified(Instant currLastModified) {
 		// Any difference indicates the path was modified.
 
-		lastModifiedChanged = lastModified != currLastModified;
+		lastModifiedChanged = !lastModified.equals(currLastModified);
 		if (lastModifiedChanged) {
+			if (LOG.isDebugEnabled()) {
+				LOG.debug(
+						"file={}, lastModified changed from {} to {}", //$NON-NLS-1$
+						file, dateFmt.format(lastModified),
+						dateFmt.format(currLastModified));
+			}
 			return true;
 		}
 
@@ -412,26 +547,40 @@ public class FileSnapshot {
 		// after the last modification that any new modifications
 		// are certain to change the last modified time.
 		if (cannotBeRacilyClean) {
+			LOG.debug("file={}, cannot be racily clean", file); //$NON-NLS-1$
 			return false;
 		}
 		if (!isRacyClean(lastRead)) {
 			// Our last read should have marked cannotBeRacilyClean,
 			// but this thread may not have seen the change. The read
 			// of the volatile field lastRead should have fixed that.
+			LOG.debug("file={}, is unmodified", file); //$NON-NLS-1$
 			return false;
 		}
 
 		// We last read this path too close to its last observed
 		// modification time. We may have missed a modification.
 		// Scan again, to ensure we still see the same state.
+		LOG.debug("file={}, is racily clean", file); //$NON-NLS-1$
 		return true;
 	}
 
 	private boolean isFileKeyChanged(Object currFileKey) {
-		return currFileKey != MISSING_FILEKEY && !currFileKey.equals(fileKey);
+		boolean changed = currFileKey != MISSING_FILEKEY
+				&& !currFileKey.equals(fileKey);
+		if (changed) {
+			LOG.debug("file={}, FileKey changed from {} to {}", //$NON-NLS-1$
+					file, fileKey, currFileKey);
+		}
+		return changed;
 	}
 
 	private boolean isSizeChanged(long currSize) {
-		return currSize != UNKNOWN_SIZE && currSize != size;
+		boolean changed = (currSize != UNKNOWN_SIZE) && (currSize != size);
+		if (changed) {
+			LOG.debug("file={}, size changed from {} to {} bytes", //$NON-NLS-1$
+					file, Long.valueOf(size), Long.valueOf(currSize));
+		}
+		return changed;
 	}
 }

org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/GC.java

@@ -371,8 +371,9 @@ public class GC {
 					continue oldPackLoop;
 
 			if (!oldPack.shouldBeKept()
-					&& repo.getFS().lastModified(
-							oldPack.getPackFile()) < packExpireDate) {
+					&& repo.getFS()
+							.lastModifiedInstant(oldPack.getPackFile())
+							.toEpochMilli() < packExpireDate) {
 				oldPack.close();
 				if (shouldLoosen) {
 					loosen(inserter, reader, oldPack, ids);
@@ -560,8 +561,10 @@ public class GC {
 					String fName = f.getName();
 					if (fName.length() != Constants.OBJECT_ID_STRING_LENGTH - 2)
 						continue;
-					if (repo.getFS().lastModified(f) >= expireDate)
+					if (repo.getFS().lastModifiedInstant(f)
+							.toEpochMilli() >= expireDate) {
 						continue;
+					}
 					try {
 						ObjectId id = ObjectId.fromString(d + fName);
 						if (objectsToKeep.contains(id))

org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/LockFile.java

@@ -56,8 +56,12 @@ import java.io.OutputStream;
 import java.nio.ByteBuffer;
 import java.nio.channels.Channels;
 import java.nio.channels.FileChannel;
+import java.nio.file.Files;
 import java.nio.file.StandardCopyOption;
+import java.nio.file.attribute.FileTime;
 import java.text.MessageFormat;
+import java.time.Instant;
+import java.util.concurrent.TimeUnit;
 
 import org.eclipse.jgit.internal.JGitText;
 import org.eclipse.jgit.lib.Constants;
@@ -400,9 +404,16 @@ public class LockFile {
 	public void waitForStatChange() throws InterruptedException {
 		FileSnapshot o = FileSnapshot.save(ref);
 		FileSnapshot n = FileSnapshot.save(lck);
+		long fsTimeResolution = FS.getFileStoreAttributes(lck.toPath())
+				.getFsTimestampResolution().toNanos();
 		while (o.equals(n)) {
-			Thread.sleep(25 /* milliseconds */);
-			lck.setLastModified(System.currentTimeMillis());
+			TimeUnit.NANOSECONDS.sleep(fsTimeResolution);
+			try {
+				Files.setLastModifiedTime(lck.toPath(),
+						FileTime.from(Instant.now()));
+			} catch (IOException e) {
+				n.waitUntilNotRacy();
+			}
 			n = FileSnapshot.save(lck);
 		}
 	}
@@ -452,11 +463,22 @@ public class LockFile {
 	 * Get the modification time of the output file when it was committed.
 	 *
 	 * @return modification time of the lock file right before we committed it.
+	 * @deprecated use {@link #getCommitLastModifiedInstant()} instead
 	 */
+	@Deprecated
 	public long getCommitLastModified() {
 		return commitSnapshot.lastModified();
 	}
 
+	/**
+	 * Get the modification time of the output file when it was committed.
+	 *
+	 * @return modification time of the lock file right before we committed it.
+	 */
+	public Instant getCommitLastModifiedInstant() {
+		return commitSnapshot.lastModifiedInstant();
+	}
+
 	/**
 	 * Get the {@link FileSnapshot} just before commit.
 	 *

org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/ObjectDirectoryPackParser.java

@@ -356,7 +356,7 @@ public class ObjectDirectoryPackParser extends PackParser {
 		buf[len++] = (byte) ((typeCode << 4) | (sz & 15));
 		sz >>>= 4;
 		while (sz > 0) {
-			buf[len - 1] |= 0x80;
+			buf[len - 1] |= (byte) 0x80;
 			buf[len++] = (byte) (sz & 0x7f);
 			sz >>>= 7;
 		}

org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackFile.java

@@ -60,6 +60,7 @@ import java.nio.channels.FileChannel.MapMode;
 import java.nio.file.AccessDeniedException;
 import java.nio.file.NoSuchFileException;
 import java.text.MessageFormat;
+import java.time.Instant;
 import java.util.Arrays;
 import java.util.Collections;
 import java.util.Comparator;
@@ -104,8 +105,12 @@ import org.slf4j.LoggerFactory;
 public class PackFile implements Iterable<PackIndex.MutableEntry> {
 	private final static Logger LOG = LoggerFactory.getLogger(PackFile.class);
 	/** Sorts PackFiles to be most recently created to least recently created. */
-	public static final Comparator<PackFile> SORT = (PackFile a,
-			PackFile b) -> b.packLastModified - a.packLastModified;
+	public static final Comparator<PackFile> SORT = new Comparator<PackFile>() {
+		@Override
+		public int compare(PackFile a, PackFile b) {
+			return b.packLastModified.compareTo(a.packLastModified);
+		}
+	};
 
 	private final File packFile;
 
@@ -128,7 +133,7 @@ public class PackFile implements Iterable<PackIndex.MutableEntry> {
 
 	private int activeCopyRawData;
 
-	int packLastModified;
+	Instant packLastModified;
 
 	private PackFileSnapshot fileSnapshot;
 
@@ -168,7 +173,7 @@ public class PackFile implements Iterable<PackIndex.MutableEntry> {
 	public PackFile(File packFile, int extensions) {
 		this.packFile = packFile;
 		this.fileSnapshot = PackFileSnapshot.save(packFile);
-		this.packLastModified = (int) (fileSnapshot.lastModified() >> 10);
+		this.packLastModified = fileSnapshot.lastModifiedInstant();
 		this.extensions = extensions;
 
 		// Multiply by 31 here so we can more directly combine with another

org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/UnpackedObjectCache.java

@@ -112,7 +112,7 @@ class UnpackedObjectCache {
 				if (obj == null)
 					break;
 
-				if (AnyObjectId.equals(obj, toFind))
+				if (AnyObjectId.isEqual(obj, toFind))
 					return true;
 
 				if (++i == ids.length())
@@ -132,7 +132,7 @@ class UnpackedObjectCache {
 						continue;
 				}
 
-				if (AnyObjectId.equals(obj, toAdd))
+				if (AnyObjectId.isEqual(obj, toAdd))
 					return true;
 
 				if (++i == ids.length())

org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/pack/BinaryDelta.java

@@ -142,7 +142,7 @@ public class BinaryDelta {
 		int c, shift = 0;
 		do {
 			c = delta[deltaPtr++] & 0xff;
-			baseLen |= ((long) (c & 0x7f)) << shift;
+			baseLen |= (c & 0x7f) << shift;
 			shift += 7;
 		} while ((c & 0x80) != 0);
 		if (base.length != baseLen)
@@ -155,7 +155,7 @@ public class BinaryDelta {
 		shift = 0;
 		do {
 			c = delta[deltaPtr++] & 0xff;
-			resLen |= ((long) (c & 0x7f)) << shift;
+			resLen |= (c & 0x7f) << shift;
 			shift += 7;
 		} while ((c & 0x80) != 0);
 

org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/pack/PackWriter.java

@@ -2198,7 +2198,7 @@ public class PackWriter implements AutoCloseable {
 		if (!cachedPacks.isEmpty()) {
 			if (otp.isEdge())
 				return;
-			if ((nFmt == PACK_WHOLE) | (nFmt == PACK_DELTA)) {
+			if (nFmt == PACK_WHOLE || nFmt == PACK_DELTA) {
 				for (CachedPack pack : cachedPacks) {
 					if (pack.hasObject(otp, next)) {
 						otp.setEdge();
@@ -2241,7 +2241,7 @@ public class PackWriter implements AutoCloseable {
 			otp.clearReuseAsIs();
 		}
 
-		otp.setDeltaAttempted(reuseDeltas & next.wasDeltaAttempted());
+		otp.setDeltaAttempted(reuseDeltas && next.wasDeltaAttempted());
 		otp.select(next);
 	}
 

org.eclipse.jgit/src/org/eclipse/jgit/internal/transport/http/NetscapeCookieFile.java

@@ -78,7 +78,7 @@ import org.slf4j.LoggerFactory;
  * Wraps all cookies persisted in a <strong>Netscape Cookie File Format</strong>
  * being referenced via the git config <a href=
  * "https://git-scm.com/docs/git-config#git-config-httpcookieFile">http.cookieFile</a>.
- *
+ * <p>
  * It will only load the cookies lazily, i.e. before calling
  * {@link #getCookies(boolean)} the file is not evaluated. This class also
  * allows persisting cookies in that file format.
@@ -134,6 +134,7 @@ public final class NetscapeCookieFile {
 
 	/**
 	 * @param path
+	 *            where to find the cookie file
 	 */
 	public NetscapeCookieFile(Path path) {
 		this(path, new Date());
@@ -146,13 +147,17 @@ public final class NetscapeCookieFile {
 	}
 
 	/**
-	 * @return the path to the underlying cookie file
+	 * Path to the underlying cookie file.
+	 *
+	 * @return the path
 	 */
 	public Path getPath() {
 		return path;
 	}
 
 	/**
+	 * Return all cookies from the underlying cookie file.
+	 *
 	 * @param refresh
 	 *            if {@code true} updates the list from the underlying cookie
 	 *            file if it has been modified since the last read otherwise
@@ -205,7 +210,7 @@ public final class NetscapeCookieFile {
 	 * @throws IOException
 	 *             if the given file could not be read for some reason
 	 * @throws IllegalArgumentException
-	 *             if the given file does not have a proper format.
+	 *             if the given file does not have a proper format
 	 */
 	private static Set<HttpCookie> parseCookieFile(@NonNull byte[] input,
 			@NonNull Date creationDate)
@@ -272,73 +277,19 @@ public final class NetscapeCookieFile {
 		return cookie;
 	}
 
-	/**
-	 * Writes all the cookies being maintained in the set being returned by
-	 * {@link #getCookies(boolean)} to the underlying file.
-	 *
-	 * Session-cookies will not be persisted.
-	 *
-	 * @param url
-	 *            url for which to write the cookies (important to derive
-	 *            default values for non-explicitly set attributes)
-	 * @throws IOException
-	 * @throws IllegalArgumentException
-	 * @throws InterruptedException
-	 */
-	public void write(URL url)
-			throws IllegalArgumentException, IOException, InterruptedException {
-		try {
-			byte[] cookieFileContent = getFileContentIfModified();
-			if (cookieFileContent != null) {
-				LOG.debug(
-						"Reading the underlying cookie file '{}' as it has been modified since the last access", //$NON-NLS-1$
-						path);
-				// reread new changes if necessary
-				Set<HttpCookie> cookiesFromFile = NetscapeCookieFile
-						.parseCookieFile(cookieFileContent, creationDate);
-				this.cookies = mergeCookies(cookiesFromFile, cookies);
-			}
-		} catch (FileNotFoundException e) {
-			// ignore if file previously did not exist yet!
-		}
-
-		ByteArrayOutputStream output = new ByteArrayOutputStream();
-		try (Writer writer = new OutputStreamWriter(output,
-				StandardCharsets.US_ASCII)) {
-			write(writer, cookies, url, creationDate);
-		}
-		LockFile lockFile = new LockFile(path.toFile());
-		for (int retryCount = 0; retryCount < LOCK_ACQUIRE_MAX_RETRY_COUNT; retryCount++) {
-			if (lockFile.lock()) {
-				try {
-					lockFile.setNeedSnapshot(true);
-					lockFile.write(output.toByteArray());
-					if (!lockFile.commit()) {
-						throw new IOException(MessageFormat.format(
-								JGitText.get().cannotCommitWriteTo, path));
-					}
-				} finally {
-					lockFile.unlock();
-				}
-				return;
-			}
-			Thread.sleep(LOCK_ACQUIRE_RETRY_SLEEP);
-		}
-		throw new IOException(
-				MessageFormat.format(JGitText.get().cannotLock, lockFile));
-
-	}
-
 	/**
 	 * Read the underying file and return its content but only in case it has
-	 * been modified since the last access. Internally calculates the hash and
-	 * maintains {@link FileSnapshot}s to prevent issues described as <a href=
+	 * been modified since the last access.
+	 * <p>
+	 * Internally calculates the hash and maintains {@link FileSnapshot}s to
+	 * prevent issues described as <a href=
 	 * "https://github.com/git/git/blob/master/Documentation/technical/racy-git.txt">"Racy
 	 * Git problem"</a>. Inspired by {@link FileBasedConfig#load()}.
 	 *
 	 * @return the file contents in case the file has been modified since the
 	 *         last access, otherwise {@code null}
 	 * @throws IOException
+	 *             if the file is not found or cannot be read
 	 */
 	private byte[] getFileContentIfModified() throws IOException {
 		final int maxStaleRetries = 5;
@@ -386,16 +337,74 @@ public final class NetscapeCookieFile {
 
 	}
 
-	private byte[] hash(final byte[] in) {
+	private static byte[] hash(final byte[] in) {
 		return Constants.newMessageDigest().digest(in);
 	}
 
+	/**
+	 * Writes all the cookies being maintained in the set being returned by
+	 * {@link #getCookies(boolean)} to the underlying file.
+	 * <p>
+	 * Session-cookies will not be persisted.
+	 *
+	 * @param url
+	 *            url for which to write the cookies (important to derive
+	 *            default values for non-explicitly set attributes)
+	 * @throws IOException
+	 *             if the underlying cookie file could not be read or written or
+	 *             a problem with the lock file
+	 * @throws InterruptedException
+	 *             if the thread is interrupted while waiting for the lock
+	 */
+	public void write(URL url) throws IOException, InterruptedException {
+		try {
+			byte[] cookieFileContent = getFileContentIfModified();
+			if (cookieFileContent != null) {
+				LOG.debug("Reading the underlying cookie file '{}' " //$NON-NLS-1$
+						+ "as it has been modified since " //$NON-NLS-1$
+						+ "the last access", //$NON-NLS-1$
+						path);
+				// reread new changes if necessary
+				Set<HttpCookie> cookiesFromFile = NetscapeCookieFile
+						.parseCookieFile(cookieFileContent, creationDate);
+				this.cookies = mergeCookies(cookiesFromFile, cookies);
+			}
+		} catch (FileNotFoundException e) {
+			// ignore if file previously did not exist yet!
+		}
+
+		ByteArrayOutputStream output = new ByteArrayOutputStream();
+		try (Writer writer = new OutputStreamWriter(output,
+				StandardCharsets.US_ASCII)) {
+			write(writer, cookies, url, creationDate);
+		}
+		LockFile lockFile = new LockFile(path.toFile());
+		for (int retryCount = 0; retryCount < LOCK_ACQUIRE_MAX_RETRY_COUNT; retryCount++) {
+			if (lockFile.lock()) {
+				try {
+					lockFile.setNeedSnapshot(true);
+					lockFile.write(output.toByteArray());
+					if (!lockFile.commit()) {
+						throw new IOException(MessageFormat.format(
+								JGitText.get().cannotCommitWriteTo, path));
+					}
+				} finally {
+					lockFile.unlock();
+				}
+				return;
+			}
+			Thread.sleep(LOCK_ACQUIRE_RETRY_SLEEP);
+		}
+		throw new IOException(
+				MessageFormat.format(JGitText.get().cannotLock, lockFile));
+	}
+
 	/**
 	 * Writes the given cookies to the file in the Netscape Cookie File Format
-	 * (also used by curl)
+	 * (also used by curl).
 	 *
 	 * @param writer
-	 *            the writer to use to persist the cookies.
+	 *            the writer to use to persist the cookies
 	 * @param cookies
 	 *            the cookies to write into the file
 	 * @param url
@@ -404,8 +413,9 @@ public final class NetscapeCookieFile {
 	 * @param creationDate
 	 *            the date when the cookie has been created. Important for
 	 *            calculation the cookie expiration time (calculated from
-	 *            cookie's maxAge and this creation time).
+	 *            cookie's maxAge and this creation time)
 	 * @throws IOException
+	 *             if an I/O error occurs
 	 */
 	static void write(@NonNull Writer writer,
 			@NonNull Collection<HttpCookie> cookies, @NonNull URL url,
@@ -461,7 +471,9 @@ public final class NetscapeCookieFile {
 	 * the entry from set {@code cookies1} ends up in the resulting set.
 	 *
 	 * @param cookies1
+	 *            first set of cookies
 	 * @param cookies2
+	 *            second set of cookies
 	 *
 	 * @return the merged cookies
 	 */

org.eclipse.jgit/src/org/eclipse/jgit/internal/transport/ssh/OpenSshConfigFile.java

@@ -50,6 +50,7 @@ import java.io.BufferedReader;
 import java.io.File;
 import java.io.IOException;
 import java.nio.file.Files;
+import java.time.Instant;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.HashMap;
@@ -65,6 +66,7 @@ import org.eclipse.jgit.annotations.NonNull;
 import org.eclipse.jgit.errors.InvalidPatternException;
 import org.eclipse.jgit.fnmatch.FileNameMatcher;
 import org.eclipse.jgit.transport.SshConstants;
+import org.eclipse.jgit.util.FS;
 import org.eclipse.jgit.util.StringUtils;
 import org.eclipse.jgit.util.SystemReader;
 
@@ -129,7 +131,7 @@ public class OpenSshConfigFile {
 	private final String localUserName;
 
 	/** Modification time of {@link #configFile} when it was last loaded. */
-	private long lastModified;
+	private Instant lastModified;
 
 	/**
 	 * Encapsulates entries read out of the configuration file, and a cache of
@@ -223,8 +225,8 @@ public class OpenSshConfigFile {
 	}
 
 	private synchronized State refresh() {
-		final long mtime = configFile.lastModified();
-		if (mtime != lastModified) {
+		final Instant mtime = FS.DETECTED.lastModifiedInstant(configFile);
+		if (!mtime.equals(lastModified)) {
 			State newState = new State();
 			try (BufferedReader br = Files
 					.newBufferedReader(configFile.toPath(), UTF_8)) {

org.eclipse.jgit/src/org/eclipse/jgit/lib/AnyObjectId.java

@@ -49,6 +49,7 @@ import java.io.Writer;
 import java.nio.ByteBuffer;
 
 import org.eclipse.jgit.util.NB;
+import org.eclipse.jgit.util.References;
 
 /**
  * A (possibly mutable) SHA-1 abstraction.
@@ -60,19 +61,37 @@ import org.eclipse.jgit.util.NB;
 public abstract class AnyObjectId implements Comparable<AnyObjectId> {
 
 	/**
-	 * Compare to object identifier byte sequences for equality.
+	 * Compare two object identifier byte sequences for equality.
 	 *
 	 * @param firstObjectId
 	 *            the first identifier to compare. Must not be null.
 	 * @param secondObjectId
 	 *            the second identifier to compare. Must not be null.
 	 * @return true if the two identifiers are the same.
+	 * @deprecated use {@link #isEqual(AnyObjectId, AnyObjectId)} instead
 	 */
+	@Deprecated
+	@SuppressWarnings("AmbiguousMethodReference")
 	public static boolean equals(final AnyObjectId firstObjectId,
 			final AnyObjectId secondObjectId) {
-		if (firstObjectId == secondObjectId)
-			return true;
+		return isEqual(firstObjectId, secondObjectId);
+	}
 
+	/**
+	 * Compare two object identifier byte sequences for equality.
+	 *
+	 * @param firstObjectId
+	 *            the first identifier to compare. Must not be null.
+	 * @param secondObjectId
+	 *            the second identifier to compare. Must not be null.
+	 * @return true if the two identifiers are the same.
+	 * @since 5.4
+	 */
+	public static boolean isEqual(final AnyObjectId firstObjectId,
+			final AnyObjectId secondObjectId) {
+		if (References.isSameObject(firstObjectId, secondObjectId)) {
+			return true;
+		}
 		// We test word 3 first since the git file-based ODB
 		// uses the first byte of w1, and we use w2 as the
 		// hash code, one of those probably came up with these
@@ -80,7 +99,6 @@ public abstract class AnyObjectId implements Comparable<AnyObjectId> {
 		// Therefore the first two words are very likely to be
 		// identical. We want to break away from collisions as
 		// quickly as possible.
-		//
 		return firstObjectId.w3 == secondObjectId.w3
 				&& firstObjectId.w4 == secondObjectId.w4
 				&& firstObjectId.w5 == secondObjectId.w5
@@ -276,8 +294,9 @@ public abstract class AnyObjectId implements Comparable<AnyObjectId> {
 	 *            the other id to compare to. May be null.
 	 * @return true only if both ObjectIds have identical bits.
 	 */
+	@SuppressWarnings({ "NonOverridingEquals", "AmbiguousMethodReference" })
 	public final boolean equals(AnyObjectId other) {
-		return other != null ? equals(this, other) : false;
+		return other != null ? isEqual(this, other) : false;
 	}
 
 	/** {@inheritDoc} */

org.eclipse.jgit/src/org/eclipse/jgit/lib/CommitBuilder.java

@@ -57,6 +57,7 @@ import java.text.MessageFormat;
 import java.util.List;
 
 import org.eclipse.jgit.internal.JGitText;
+import org.eclipse.jgit.util.References;
 
 /**
  * Mutable builder to construct a commit recording the state of a project.
@@ -365,7 +366,7 @@ public class CommitBuilder {
 				os.write('\n');
 			}
 
-			if (getEncoding() != UTF_8) {
+			if (!References.isSameObject(getEncoding(), UTF_8)) {
 				os.write(hencoding);
 				os.write(' ');
 				os.write(Constants.encodeASCII(getEncoding().name()));
@@ -474,7 +475,7 @@ public class CommitBuilder {
 		r.append(gpgSignature != null ? gpgSignature.toString() : "NOT_SET");
 		r.append("\n");
 
-		if (encoding != null && encoding != UTF_8) {
+		if (encoding != null && !References.isSameObject(encoding, UTF_8)) {
 			r.append("encoding ");
 			r.append(encoding.name());
 			r.append("\n");

org.eclipse.jgit/src/org/eclipse/jgit/lib/Config.java

@@ -131,10 +131,11 @@ public class Config {
 	/**
 	 * Check if a given string is the "missing" value.
 	 *
-	 * @param value
+	 * @param value string to be checked.
 	 * @return true if the given string is the "missing" value.
 	 * @since 5.4
 	 */
+	@SuppressWarnings({ "ReferenceEquality", "StringEquality" })
 	public static boolean isMissing(String value) {
 		return value == MISSING_ENTRY;
 	}
@@ -1052,7 +1053,7 @@ public class Config {
 				if (e.prefix == null || "".equals(e.prefix)) //$NON-NLS-1$
 					out.append('\t');
 				out.append(e.name);
-				if (MISSING_ENTRY != e.value) {
+				if (!isMissing(e.value)) {
 					out.append(" ="); //$NON-NLS-1$
 					if (e.value != null) {
 						out.append(' ');

org.eclipse.jgit/src/org/eclipse/jgit/lib/ConfigConstants.java

@@ -476,4 +476,23 @@ public final class ConfigConstants {
 	 * @since 5.2
 	 */
 	public static final String CONFIG_KEY_LOG_OUTPUT_ENCODING = "logOutputEncoding";
+
+	/**
+	 * The "filesystem" section
+	 * @since 5.1.9
+	 */
+	public static final String CONFIG_FILESYSTEM_SECTION = "filesystem";
+
+	/**
+	 * The "timestampResolution" key
+	 * @since 5.1.9
+	 */
+	public static final String CONFIG_KEY_TIMESTAMP_RESOLUTION = "timestampResolution";
+
+	/**
+	 * The "minRacyThreshold" key
+	 *
+	 * @since 5.1.9
+	 */
+	public static final String CONFIG_KEY_MIN_RACY_THRESHOLD = "minRacyThreshold";
 }

org.eclipse.jgit/src/org/eclipse/jgit/lib/DefaultTypedConfigGetter.java

@@ -226,6 +226,14 @@ public class DefaultTypedConfigGetter implements TypedConfigGetter {
 			inputUnit = wantUnit;
 			inputMul = 1;
 
+		} else if (match(unitName, "ns", "nanoseconds")) { //$NON-NLS-1$ //$NON-NLS-2$
+			inputUnit = TimeUnit.NANOSECONDS;
+			inputMul = 1;
+
+		} else if (match(unitName, "us", "microseconds")) { //$NON-NLS-1$ //$NON-NLS-2$
+			inputUnit = TimeUnit.MICROSECONDS;
+			inputMul = 1;
+
 		} else if (match(unitName, "ms", "milliseconds")) { //$NON-NLS-1$ //$NON-NLS-2$
 			inputUnit = TimeUnit.MILLISECONDS;
 			inputMul = 1;

org.eclipse.jgit/src/org/eclipse/jgit/lib/FileMode.java

@@ -88,6 +88,7 @@ public abstract class FileMode {
 	public static final FileMode TREE = new FileMode(TYPE_TREE,
 			Constants.OBJ_TREE) {
 		@Override
+		@SuppressWarnings("NonOverridingEquals")
 		public boolean equals(int modeBits) {
 			return (modeBits & TYPE_MASK) == TYPE_TREE;
 		}
@@ -97,6 +98,7 @@ public abstract class FileMode {
 	public static final FileMode SYMLINK = new FileMode(TYPE_SYMLINK,
 			Constants.OBJ_BLOB) {
 		@Override
+		@SuppressWarnings("NonOverridingEquals")
 		public boolean equals(int modeBits) {
 			return (modeBits & TYPE_MASK) == TYPE_SYMLINK;
 		}
@@ -106,6 +108,7 @@ public abstract class FileMode {
 	public static final FileMode REGULAR_FILE = new FileMode(0100644,
 			Constants.OBJ_BLOB) {
 		@Override
+		@SuppressWarnings("NonOverridingEquals")
 		public boolean equals(int modeBits) {
 			return (modeBits & TYPE_MASK) == TYPE_FILE && (modeBits & 0111) == 0;
 		}
@@ -115,6 +118,7 @@ public abstract class FileMode {
 	public static final FileMode EXECUTABLE_FILE = new FileMode(0100755,
 			Constants.OBJ_BLOB) {
 		@Override
+		@SuppressWarnings("NonOverridingEquals")
 		public boolean equals(int modeBits) {
 			return (modeBits & TYPE_MASK) == TYPE_FILE && (modeBits & 0111) != 0;
 		}
@@ -124,6 +128,7 @@ public abstract class FileMode {
 	public static final FileMode GITLINK = new FileMode(TYPE_GITLINK,
 			Constants.OBJ_COMMIT) {
 		@Override
+		@SuppressWarnings("NonOverridingEquals")
 		public boolean equals(int modeBits) {
 			return (modeBits & TYPE_MASK) == TYPE_GITLINK;
 		}
@@ -133,6 +138,7 @@ public abstract class FileMode {
 	public static final FileMode MISSING = new FileMode(TYPE_MISSING,
 			Constants.OBJ_BAD) {
 		@Override
+		@SuppressWarnings("NonOverridingEquals")
 		public boolean equals(int modeBits) {
 			return modeBits == 0;
 		}
@@ -165,6 +171,7 @@ public abstract class FileMode {
 
 		return new FileMode(bits, Constants.OBJ_BAD) {
 			@Override
+			@SuppressWarnings("NonOverridingEquals")
 			public boolean equals(int a) {
 				return bits == a;
 			}
@@ -206,6 +213,7 @@ public abstract class FileMode {
 	 *            a int.
 	 * @return true if the mode bits represent the same mode as this object
 	 */
+	@SuppressWarnings("NonOverridingEquals")
 	public abstract boolean equals(int modebits);
 
 	/**

org.eclipse.jgit/src/org/eclipse/jgit/lib/IndexDiff.java

@@ -642,11 +642,12 @@ public class IndexDiff {
 	private void addConflict(String path, int stage) {
 		StageState existingStageStates = conflicts.get(path);
 		byte stageMask = 0;
-		if (existingStageStates != null)
-			stageMask |= existingStageStates.getStageMask();
+		if (existingStageStates != null) {
+			stageMask |= (byte) existingStageStates.getStageMask();
+		}
 		// stage 1 (base) should be shifted 0 times
 		int shifts = stage - 1;
-		stageMask |= (1 << shifts);
+		stageMask |= (byte) (1 << shifts);
 		StageState stageState = StageState.fromMask(stageMask);
 		conflicts.put(path, stageState);
 	}

org.eclipse.jgit/src/org/eclipse/jgit/lib/ObjectIdSubclassMap.java

@@ -103,8 +103,9 @@ public class ObjectIdSubclassMap<V extends ObjectId>
 		V obj;
 
 		while ((obj = tbl[i]) != null) {
-			if (AnyObjectId.equals(obj, toFind))
+			if (AnyObjectId.isEqual(obj, toFind)) {
 				return obj;
+			}
 			i = (i + 1) & msk;
 		}
 		return null;
@@ -162,7 +163,7 @@ public class ObjectIdSubclassMap<V extends ObjectId>
 		V obj;
 
 		while ((obj = tbl[i]) != null) {
-			if (AnyObjectId.equals(obj, newValue))
+			if (AnyObjectId.isEqual(obj, newValue))
 				return obj;
 			i = (i + 1) & msk;
 		}