diff --git a/lib/BUILD b/lib/BUILD
index f41ad16..932d7df 100644
--- a/lib/BUILD
+++ b/lib/BUILD
@@ -12,6 +12,7 @@
     visibility = [
         "//org.eclipse.jgit.archive:__pkg__",
         "//org.eclipse.jgit.pgm.test:__pkg__",
+        "//org.eclipse.jgit.test:__pkg__",
     ],
     exports = ["@commons-compress//jar"],
 )
diff --git a/org.eclipse.jgit.ant.test/src/org/eclipse/jgit/ant/tasks/GitCloneTaskTest.java b/org.eclipse.jgit.ant.test/src/org/eclipse/jgit/ant/tasks/GitCloneTaskTest.java
index 3ce0663..8043d2b 100644
--- a/org.eclipse.jgit.ant.test/src/org/eclipse/jgit/ant/tasks/GitCloneTaskTest.java
+++ b/org.eclipse.jgit.ant.test/src/org/eclipse/jgit/ant/tasks/GitCloneTaskTest.java
@@ -65,12 +65,13 @@
 
 	@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);
 	}
 
diff --git a/org.eclipse.jgit.ant/META-INF/MANIFEST.MF b/org.eclipse.jgit.ant/META-INF/MANIFEST.MF
index 8dd0daa..41a0422 100644
--- a/org.eclipse.jgit.ant/META-INF/MANIFEST.MF
+++ b/org.eclipse.jgit.ant/META-INF/MANIFEST.MF
@@ -9,5 +9,7 @@
   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"
diff --git a/org.eclipse.jgit.archive/META-INF/MANIFEST.MF b/org.eclipse.jgit.archive/META-INF/MANIFEST.MF
index 23e32fc..965c798 100644
--- a/org.eclipse.jgit.archive/META-INF/MANIFEST.MF
+++ b/org.eclipse.jgit.archive/META-INF/MANIFEST.MF
@@ -26,4 +26,4 @@
    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
diff --git a/org.eclipse.jgit.http.server/src/org/eclipse/jgit/http/server/FileSender.java b/org.eclipse.jgit.http.server/src/org/eclipse/jgit/http/server/FileSender.java
index 05510a0..946fb15 100644
--- a/org.eclipse.jgit.http.server/src/org/eclipse/jgit/http/server/FileSender.java
+++ b/org.eclipse.jgit.http.server/src/org/eclipse/jgit/http/server/FileSender.java
@@ -58,12 +58,14 @@
 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 @@
 
 	private final RandomAccessFile source;
 
-	private final long lastModified;
+	private final Instant lastModified;
 
 	private final long fileLen;
 
@@ -89,7 +91,7 @@
 		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 @@
 		}
 	}
 
-	long getLastModified() {
+	Instant getLastModified() {
 		return lastModified;
 	}
 
diff --git a/org.eclipse.jgit.http.server/src/org/eclipse/jgit/http/server/ObjectFileServlet.java b/org.eclipse.jgit.http.server/src/org/eclipse/jgit/http/server/ObjectFileServlet.java
index 62f075c..5a27be6 100644
--- a/org.eclipse.jgit.http.server/src/org/eclipse/jgit/http/server/ObjectFileServlet.java
+++ b/org.eclipse.jgit.http.server/src/org/eclipse/jgit/http/server/ObjectFileServlet.java
@@ -54,6 +54,7 @@
 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 @@
 
 		@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 @@
 
 		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)) {
diff --git a/org.eclipse.jgit.junit/.settings/org.eclipse.jdt.core.prefs b/org.eclipse.jgit.junit/.settings/org.eclipse.jdt.core.prefs
index 2ca78ff..b675029 100644
--- a/org.eclipse.jgit.junit/.settings/org.eclipse.jdt.core.prefs
+++ b/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.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.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.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.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
diff --git a/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/LocalDiskRepositoryTestCase.java b/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/LocalDiskRepositoryTestCase.java
index f93424c..98e1f82 100644
--- a/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/LocalDiskRepositoryTestCase.java
+++ b/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/LocalDiskRepositoryTestCase.java
@@ -51,6 +51,8 @@
 
 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 @@
 		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 @@
 	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 @@
 			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 @@
 				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())
diff --git a/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/Repeat.java b/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/Repeat.java
index 08220ce..94df554 100644
--- a/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/Repeat.java
+++ b/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/Repeat.java
@@ -56,4 +56,13 @@
 	 * 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;
 }
diff --git a/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/RepeatRule.java b/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/RepeatRule.java
index 8165738..8636f2a 100644
--- a/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/RepeatRule.java
+++ b/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/RepeatRule.java
@@ -81,9 +81,31 @@
 	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 @@
 
 		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 @@
 		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;
 	}
diff --git a/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/RepositoryTestCase.java b/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/RepositoryTestCase.java
index a5270ed..23f49a4 100644
--- a/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/RepositoryTestCase.java
+++ b/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/RepositoryTestCase.java
@@ -57,7 +57,9 @@
 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 @@
 
 				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 @@
 	 * @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 @@
 			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 {
diff --git a/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/TestRepository.java b/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/TestRepository.java
index 356d9d8..e89cf0f 100644
--- a/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/TestRepository.java
+++ b/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/TestRepository.java
@@ -728,7 +728,7 @@
 		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 @@
 			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 @@
 			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 @@
 			});
 		}
 
+		/**
+		 * 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 @@
 			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 @@
 			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 @@
 			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 @@
 						+ 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);
 		}
diff --git a/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/time/TimeUtil.java b/org.eclipse.jgit.junit/src/org/eclipse/jgit/junit/time/TimeUtil.java
new file mode 100644
index 0000000..1f8070d
--- /dev/null
+++ b/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);
+		}
+	}
+
+}
diff --git a/org.eclipse.jgit.lfs.server.test/tst/org/eclipse/jgit/lfs/server/fs/LfsServerTest.java b/org.eclipse.jgit.lfs.server.test/tst/org/eclipse/jgit/lfs/server/fs/LfsServerTest.java
index 10823b8..ec44da4 100644
--- a/org.eclipse.jgit.lfs.server.test/tst/org/eclipse/jgit/lfs/server/fs/LfsServerTest.java
+++ b/org.eclipse.jgit.lfs.server.test/tst/org/eclipse/jgit/lfs/server/fs/LfsServerTest.java
@@ -82,6 +82,7 @@
 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 @@
 	@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");
diff --git a/org.eclipse.jgit.lfs/.settings/.api_filters b/org.eclipse.jgit.lfs/.settings/.api_filters
new file mode 100644
index 0000000..9747df8
--- /dev/null
+++ b/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>
diff --git a/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/lib/AnyLongObjectId.java b/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/lib/AnyLongObjectId.java
index 0788922..b095d20 100644
--- a/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/lib/AnyLongObjectId.java
+++ b/org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/lib/AnyLongObjectId.java
@@ -50,6 +50,7 @@
 
 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 @@
 	 * @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 @@
 	 *            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;
 	}
diff --git a/org.eclipse.jgit.packaging/pom.xml b/org.eclipse.jgit.packaging/pom.xml
index bbb0f90..1e17c9d 100644
--- a/org.eclipse.jgit.packaging/pom.xml
+++ b/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>
@@ -290,6 +286,21 @@
           <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>
           <version>${tycho-extras-version}</version>
@@ -309,6 +320,25 @@
           <artifactId>build-helper-maven-plugin</artifactId>
           <version>3.0.0</version>
         </plugin>
+        <plugin>
+          <artifactId>maven-clean-plugin</artifactId>
+          <version>3.1.0</version>
+        </plugin>
+        <plugin>
+          <groupId>org.apache.maven.plugins</groupId>
+          <artifactId>maven-deploy-plugin</artifactId>
+          <version>3.0.0-M1</version>
+        </plugin>
+        <plugin>
+          <groupId>org.apache.maven.plugins</groupId>
+          <artifactId>maven-install-plugin</artifactId>
+          <version>3.0.0-M1</version>
+        </plugin>
+        <plugin>
+          <groupId>org.apache.maven.plugins</groupId>
+          <artifactId>maven-site-plugin</artifactId>
+          <version>3.7.1</version>
+        </plugin>
       </plugins>
     </pluginManagement>
   </build>
diff --git a/org.eclipse.jgit.pgm/pom.xml b/org.eclipse.jgit.pgm/pom.xml
index 12ccadd..c6af997 100644
--- a/org.eclipse.jgit.pgm/pom.xml
+++ b/org.eclipse.jgit.pgm/pom.xml
@@ -142,6 +142,12 @@
       <artifactId>org.eclipse.jgit.lfs.server</artifactId>
       <version>${project.version}</version>
     </dependency>
+
+    <dependency>
+      <groupId>org.tukaani</groupId>
+      <artifactId>xz</artifactId>
+      <optional>true</optional>
+    </dependency>
   </dependencies>
 
   <build>
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Blame.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Blame.java
index 8794ca6..e38cb46 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Blame.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Blame.java
@@ -218,7 +218,8 @@
 					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 @@
 					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();
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/TextBuiltin.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/TextBuiltin.java
index 05f2378..d81a3ae 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/TextBuiltin.java
+++ b/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;
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/ShowDirCache.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/ShowDirCache.java
index 7f99d76..14a60a3 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/ShowDirCache.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/ShowDirCache.java
@@ -48,8 +48,10 @@
 
 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 @@
 	/** {@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(' ');
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/VerifyReftable.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/VerifyReftable.java
index b38de14..15b6ff9 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/VerifyReftable.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/VerifyReftable.java
@@ -189,7 +189,7 @@
 			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 @@
 		}
 
 		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()),
diff --git a/org.eclipse.jgit.test/BUILD b/org.eclipse.jgit.test/BUILD
index 1d03afe..fc8c53c 100644
--- a/org.eclipse.jgit.test/BUILD
+++ b/org.eclipse.jgit.test/BUILD
@@ -24,7 +24,6 @@
     "revwalk/RevWalkTestCase.java",
     "transport/ObjectIdMatcher.java",
     "transport/SpiTransport.java",
-    "treewalk/FileTreeIteratorWithTimeControl.java",
     "treewalk/filter/AlwaysCloneTreeFilter.java",
     "test/resources/SampleDataRepositoryTestCase.java",
     "util/CPUTimeStopWatch.java",
diff --git a/org.eclipse.jgit.test/META-INF/MANIFEST.MF b/org.eclipse.jgit.test/META-INF/MANIFEST.MF
index 0f65c88..53b79b0 100644
--- a/org.eclipse.jgit.test/META-INF/MANIFEST.MF
+++ b/org.eclipse.jgit.test/META-INF/MANIFEST.MF
@@ -11,10 +11,17 @@
 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 @@
  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 @@
  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"
diff --git a/org.eclipse.jgit.test/pom.xml b/org.eclipse.jgit.test/pom.xml
index 99e6fe3..5e8a3e6 100644
--- a/org.eclipse.jgit.test/pom.xml
+++ b/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>
diff --git a/org.eclipse.jgit.test/tests.bzl b/org.eclipse.jgit.test/tests.bzl
index 17a45ca..f27efcc 100644
--- a/org.eclipse.jgit.test/tests.bzl
+++ b/org.eclipse.jgit.test/tests.bzl
@@ -58,6 +58,12 @@
             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"
diff --git a/org.eclipse.jgit.test/tst-rsrc/log4j.properties b/org.eclipse.jgit.test/tst-rsrc/log4j.properties
index 14620ff..ee1ac35 100644
--- a/org.eclipse.jgit.test/tst-rsrc/log4j.properties
+++ b/org.eclipse.jgit.test/tst-rsrc/log4j.properties
@@ -7,3 +7,8 @@
 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
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/AddCommandTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/AddCommandTest.java
index 3fee51a..b28e26a 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/AddCommandTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/AddCommandTest.java
@@ -1267,7 +1267,7 @@
 		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);
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/ArchiveCommandTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/ArchiveCommandTest.java
index 1c41018..0f2e6b8 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/ArchiveCommandTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/ArchiveCommandTest.java
@@ -47,20 +47,44 @@
 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 @@
 
 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 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 @@
 		}
 	}
 
+	@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> {
 
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CheckoutCommandTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CheckoutCommandTest.java
index 98a8adc..1f3527f 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CheckoutCommandTest.java
+++ b/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.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.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.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 @@
 
 		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 @@
 		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 @@
 		entry = cache.getEntry("Test.txt");
 		assertNotNull(entry);
 		assertEquals(size, entry.getLength());
-		assertEquals(mTime, entry.getLastModified());
+		assertEquals(mTime, entry.getLastModifiedInstant());
 	}
 
 	@Test
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CommitCommandTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CommitCommandTest.java
index 18fed4b..3bde0eb 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CommitCommandTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/CommitCommandTest.java
@@ -65,6 +65,7 @@
 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 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 @@
 			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 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 @@
 			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());
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/DiffCommandTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/DiffCommandTest.java
index 43c3a8c..3a93839 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/DiffCommandTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/DiffCommandTest.java
@@ -44,7 +44,6 @@
 
 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 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 @@
 	@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");
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/ResetCommandTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/ResetCommandTest.java
index 333ebd3..563b32d 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/ResetCommandTest.java
+++ 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 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 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 @@
 		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 @@
 
 		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
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/dircache/DirCacheBuilderTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/dircache/DirCacheBuilderTest.java
index 0c1131b..cdf86f0 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/dircache/DirCacheBuilderTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/dircache/DirCacheBuilderTest.java
@@ -53,6 +53,7 @@
 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 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 @@
 			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 @@
 			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 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 @@
 			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 @@
 			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 @@
 		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;
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/dircache/DirCacheEntryTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/dircache/DirCacheEntryTest.java
index 86e2852..475819d 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/dircache/DirCacheEntryTest.java
+++ b/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 @@
 		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 @@
 		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 @@
 				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());
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/dfs/DfsGarbageCollectorTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/dfs/DfsGarbageCollectorTest.java
index bfa30d5..5a5ae1d 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/dfs/DfsGarbageCollectorTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/dfs/DfsGarbageCollectorTest.java
@@ -976,7 +976,7 @@
 				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;
 				}
 			}
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/BatchRefUpdateTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/BatchRefUpdateTest.java
index 3c4b8cf..501b788 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/BatchRefUpdateTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/BatchRefUpdateTest.java
@@ -938,6 +938,7 @@
 		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) {
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/ConcurrentRepackTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/ConcurrentRepackTest.java
index 643daa5..6bec056 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/ConcurrentRepackTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/ConcurrentRepackTest.java
@@ -56,6 +56,7 @@
 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.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 @@
 
 	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 @@
 	}
 
 	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 @@
 		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());
 		}
 	}
 
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/FileSnapshotTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/FileSnapshotTest.java
index 5ebdeb6..6fa35d6 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/FileSnapshotTest.java
+++ b/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 @@
 	 */
 	@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 @@
 	 */
 	@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 @@
 	 */
 	@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 @@
 	@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 @@
 	 */
 	@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));
 	}
 
-	private static void append(File f, byte b) throws IOException {
-		try (FileOutputStream os = new FileOutputStream(f, true)) {
+	@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(Path f, byte b) throws IOException {
+		try (OutputStream os = Files.newOutputStream(f,
+				StandardOpenOption.APPEND)) {
 			os.write(b);
 		}
 	}
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/GcTestCase.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/GcTestCase.java
index d16998d..eaa245b 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/GcTestCase.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/GcTestCase.java
@@ -147,9 +147,10 @@
 		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 {
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/ObjectDirectoryTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/ObjectDirectoryTest.java
index a9d0dc2..97c5638 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/ObjectDirectoryTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/ObjectDirectoryTest.java
@@ -65,6 +65,7 @@
 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 @@
 
 			// 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));
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/PackFileSnapshotTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/PackFileSnapshotTest.java
index a1433e9..d5bc61a 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/PackFileSnapshotTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/PackFileSnapshotTest.java
@@ -59,6 +59,7 @@
 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.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 @@
 		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 @@
 		// 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 @@
 		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 @@
 		// 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 @@
 		// 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 @@
 		// 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());
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/RefDirectoryTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/RefDirectoryTest.java
index bd9572b..d8e1685 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/RefDirectoryTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/RefDirectoryTest.java
@@ -60,6 +60,7 @@
 
 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.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.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 @@
 		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 @@
 	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) {
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/T0003_BasicTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/T0003_BasicTest.java
index 825d15b..43f30d8 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/T0003_BasicTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/T0003_BasicTest.java
@@ -59,6 +59,7 @@
 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.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 @@
 	 *
 	 * @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)));
 	}
 }
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/ConfigTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/ConfigTest.java
index e3985cc..e839545 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/ConfigTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/ConfigTest.java
@@ -51,8 +51,10 @@
 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 @@
 
 	@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));
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/IndexModificationTimesTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/IndexModificationTimesTest.java
index b9bbbeb..a363414 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/IndexModificationTimesTest.java
+++ b/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 @@
 			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 @@
 			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 @@
 			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 @@
 			dc = db.readDirCache();
 			entry = dc.getEntry(path);
 
-			long sideLastMode = entry.getLastModified();
+			Instant sideLastMod = entry.getLastModifiedInstant();
 
 			Thread.sleep(2000);
 
@@ -120,9 +124,10 @@
 			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));
 		}
 	}
 
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/RacyGitTests.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/RacyGitTests.java
index 11100b6..d3e4efe 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/RacyGitTests.java
+++ b/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 @@
 		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 @@
 		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));
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/merge/MergerTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/merge/MergerTest.java
index f6fc00c..62495fb 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/merge/MergerTest.java
+++ b/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.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 @@
 	 * 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 @@
 	@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 @@
 		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 @@
 		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 @@
 		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 @@
 				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 @@
 		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 @@
 			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 @@
 	// 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);
+			}
 		}
 	}
 
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/revwalk/RevObjectTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/revwalk/RevObjectTest.java
index 4969305..e397220 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/revwalk/RevObjectTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/revwalk/RevObjectTest.java
@@ -89,8 +89,8 @@
 		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
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/storage/file/FileBasedConfigTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/storage/file/FileBasedConfigTest.java
index b401d2b..4364820 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/storage/file/FileBasedConfigTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/storage/file/FileBasedConfigTest.java
@@ -46,12 +46,13 @@
 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 @@
 	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 @@
 		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 @@
 		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 @@
 		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 @@
 		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 @@
 	@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 @@
 	@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 @@
 	@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 @@
 	@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 @@
 			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 @@
 		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 @@
 		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;
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/OpenSshConfigTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/OpenSshConfigTest.java
index 1a22e10..2e5027f 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/OpenSshConfigTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/transport/OpenSshConfigTest.java
@@ -56,10 +56,13 @@
 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 @@
 	}
 
 	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
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/treewalk/FileTreeIteratorTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/treewalk/FileTreeIteratorTest.java
index 0303ea2..a3ce4ae 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/treewalk/FileTreeIteratorTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/treewalk/FileTreeIteratorTest.java
@@ -54,6 +54,7 @@
 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 @@
 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 @@
 		// 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 @@
 		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 @@
 		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 @@
 		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 @@
 		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 @@
 	@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
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/treewalk/FileTreeIteratorWithTimeControl.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/treewalk/FileTreeIteratorWithTimeControl.java
deleted file mode 100644
index fc79d45..0000000
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/treewalk/FileTreeIteratorWithTimeControl.java
+++ /dev/null
@@ -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();
-	}
-}
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/FSTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/FSTest.java
index 6dfa6ef..99d4351 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/FSTest.java
+++ b/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 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 @@
 		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 @@
 		// 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 @@
 				.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 @@
 			}
 		}
 	}
+
+	// bug 548682
+	@Test
+	public void testRepoCacheRelativePathUnbornRepo() {
+		assertFalse(RepositoryCache.FileKey
+				.isGitRepository(new File("repo.git"), FS.DETECTED));
+	}
 }
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/SimpleLruCacheTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/SimpleLruCacheTest.java
new file mode 100644
index 0000000..5894f7d
--- /dev/null
+++ b/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"));
+	}
+}
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/StatsTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/StatsTest.java
new file mode 100644
index 0000000..8b25382
--- /dev/null
+++ b/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);
+	}
+}
diff --git a/org.eclipse.jgit.ui/src/org/eclipse/jgit/awtui/CommitGraphPane.java b/org.eclipse.jgit.ui/src/org/eclipse/jgit/awtui/CommitGraphPane.java
index 943a325..b898caf 100644
--- a/org.eclipse.jgit.ui/src/org/eclipse/jgit/awtui/CommitGraphPane.java
+++ b/org.eclipse.jgit.ui/src/org/eclipse/jgit/awtui/CommitGraphPane.java
@@ -64,6 +64,7 @@
 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 @@
 		}
 
 		PersonIdent authorFor(PlotCommit<SwingLane> c) {
-			if (c != lastCommit) {
+			if (!References.isSameObject(c, lastCommit)) {
 				lastCommit = c;
 				lastAuthor = c.getAuthorIdent();
 			}
diff --git a/org.eclipse.jgit/.settings/.api_filters b/org.eclipse.jgit/.settings/.api_filters
new file mode 100644
index 0000000..3a5dd11
--- /dev/null
+++ b/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$FileStoreAttributes">
+        <filter id="1142947843">
+            <message_arguments>
+                <message_argument value="5.1.9"/>
+                <message_argument value="FileStoreAttributes"/>
+            </message_arguments>
+        </filter>
+    </resource>
+    <resource path="src/org/eclipse/jgit/util/References.java" type="org.eclipse.jgit.util.References">
+        <filter id="1108344834">
+            <message_arguments>
+                <message_argument value="5.4"/>
+                <message_argument value="5.5"/>
+                <message_argument value="org.eclipse.jgit.util.References"/>
+            </message_arguments>
+        </filter>
+    </resource>
+    <resource path="src/org/eclipse/jgit/util/SimpleLruCache.java" type="org.eclipse.jgit.util.SimpleLruCache">
+        <filter id="1109393411">
+            <message_arguments>
+                <message_argument value="5.1.9"/>
+                <message_argument value="org.eclipse.jgit.util.SimpleLruCache"/>
+            </message_arguments>
+        </filter>
+    </resource>
+    <resource path="src/org/eclipse/jgit/util/Stats.java" type="org.eclipse.jgit.util.Stats">
+        <filter id="1109393411">
+            <message_arguments>
+                <message_argument value="5.1.9"/>
+                <message_argument value="org.eclipse.jgit.util.Stats"/>
+            </message_arguments>
+        </filter>
+    </resource>
+</component>
diff --git a/org.eclipse.jgit/pom.xml b/org.eclipse.jgit/pom.xml
index 3ea730b..cd187bf 100644
--- a/org.eclipse.jgit/pom.xml
+++ b/org.eclipse.jgit/pom.xml
@@ -223,6 +223,7 @@
         <plugin>
           <groupId>com.github.spotbugs</groupId>
           <artifactId>spotbugs-maven-plugin</artifactId>
+          <version>${spotbugs-maven-plugin-version}</version>
           <configuration>
             <excludeFilterFile>findBugs/FindBugsExcludeFilter.xml</excludeFilterFile>
           </configuration>
diff --git a/org.eclipse.jgit/resources/org/eclipse/jgit/internal/JGitText.properties b/org.eclipse.jgit/resources/org/eclipse/jgit/internal/JGitText.properties
index b610deb..e26163e 100644
--- a/org.eclipse.jgit/resources/org/eclipse/jgit/internal/JGitText.properties
+++ b/org.eclipse.jgit/resources/org/eclipse/jgit/internal/JGitText.properties
@@ -105,6 +105,7 @@
 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 @@
 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 @@
 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 @@
 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)?
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/AddCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/AddCommand.java
index f0408ab..a2cd4ae 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/AddCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/AddCommand.java
@@ -50,6 +50,7 @@
 
 import java.io.IOException;
 import java.io.InputStream;
+import java.time.Instant;
 import java.util.Collection;
 import java.util.LinkedList;
 
@@ -228,7 +229,7 @@
 
 				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 @@
 					}
 				} else {
 					entry.setLength(0);
-					entry.setLastModified(0);
+					entry.setLastModified(Instant.ofEpochSecond(0));
 					entry.setObjectId(f.getEntryObjectId());
 				}
 				builder.add(entry);
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/ArchiveCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/ArchiveCommand.java
index 27bb5a9..3f7306b 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/ArchiveCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/ArchiveCommand.java
@@ -56,13 +56,18 @@
 
 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 @@
 				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 @@
 					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 @@
 		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;
+	}
+
 }
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/CherryPickCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/CherryPickCommand.java
index 65b72f7..c9dd547 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/CherryPickCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/CherryPickCommand.java
@@ -157,8 +157,8 @@
 				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(),
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/CommitCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/CommitCommand.java
index 8671800..b55987e 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/CommitCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/CommitCommand.java
@@ -413,7 +413,7 @@
 						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
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/RebaseCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/RebaseCommand.java
index 593874c..0dacd4d 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/RebaseCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/RebaseCommand.java
@@ -575,7 +575,7 @@
 			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
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/ResetCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/ResetCommand.java
index 13ce4e7..d7c9ad5 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/ResetCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/ResetCommand.java
@@ -422,7 +422,7 @@
 						DirCacheIterator.class);
 				if (dcIter != null && dcIter.idEqual(cIter)) {
 					DirCacheEntry indexEntry = dcIter.getDirCacheEntry();
-					entry.setLastModified(indexEntry.getLastModified());
+					entry.setLastModified(indexEntry.getLastModifiedInstant());
 					entry.setLength(indexEntry.getLength());
 				}
 
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/RevertCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/RevertCommand.java
index 46e0df7..ddd60b6 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/RevertCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/RevertCommand.java
@@ -175,8 +175,8 @@
 						+ "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(),
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/StashApplyCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/StashApplyCommand.java
index 2136e51..aeb9395 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/StashApplyCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/StashApplyCommand.java
@@ -362,7 +362,7 @@
 						DirCacheIterator.class);
 				if (dcIter != null && dcIter.idEqual(cIter)) {
 					DirCacheEntry indexEntry = dcIter.getDirCacheEntry();
-					entry.setLastModified(indexEntry.getLastModified());
+					entry.setLastModified(indexEntry.getLastModifiedInstant());
 					entry.setLength(indexEntry.getLength());
 				}
 
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/StashCreateCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/StashCreateCommand.java
index c32890d..0d010ad 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/StashCreateCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/StashCreateCommand.java
@@ -300,7 +300,8 @@
 						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()) {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/dircache/DirCache.java b/org.eclipse.jgit/src/org/eclipse/jgit/dircache/DirCache.java
index eeab03d..95e1d21 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/dircache/DirCache.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/dircache/DirCache.java
@@ -58,6 +58,7 @@
 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 @@
 			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 @@
 		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 @@
 			// 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 @@
 				DirCacheEntry entry = iIter.getDirCacheEntry();
 				if (entry.isSmudged() && iIter.idEqual(fIter)) {
 					entry.setLength(fIter.getEntryLength());
-					entry.setLastModified(fIter.getEntryLastModified());
+					entry.setLastModified(fIter.getEntryLastModifiedInstant());
 				}
 			}
 		}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/dircache/DirCacheCheckout.java b/org.eclipse.jgit/src/org/eclipse/jgit/dircache/DirCacheCheckout.java
index 3b2e74e..6bc2946 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/dircache/DirCacheCheckout.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/dircache/DirCacheCheckout.java
@@ -50,6 +50,7 @@
 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 @@
 					// 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 @@
 		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 @@
 			}
 			fs.createSymLink(f, target);
 			entry.setLength(bytes.length);
-			entry.setLastModified(fs.lastModified(f));
+			entry.setLastModified(fs.lastModifiedInstant(f));
 			return;
 		}
 
@@ -1546,7 +1549,7 @@
 				FileUtils.delete(tmpFile);
 			}
 		}
-		entry.setLastModified(fs.lastModified(f));
+		entry.setLastModified(fs.lastModifiedInstant(f));
 	}
 
 	// Run an external filter command
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/dircache/DirCacheEntry.java b/org.eclipse.jgit/src/org/eclipse/jgit/dircache/DirCacheEntry.java
index 6b1d4f4..d4db15c 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/dircache/DirCacheEntry.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/dircache/DirCacheEntry.java
@@ -56,6 +56,7 @@
 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 @@
 	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 @@
 			md.update(nullpad, 0, padLen);
 		}
 
-		if (mightBeRacilyClean(smudge_s, smudge_ns))
+		if (mightBeRacilyClean(smudge)) {
 			smudgeRacilyClean();
+		}
 	}
 
 	/**
@@ -344,8 +346,29 @@
 	 * @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 @@
 		//
 		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 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 void setUpdateNeeded(boolean updateNeeded) {
 		if (updateNeeded)
-			inCoreFlags |= UPDATE_NEEDED;
+			inCoreFlags |= (byte) UPDATE_NEEDED;
 		else
-			inCoreFlags &= ~UPDATE_NEEDED;
+			inCoreFlags &= (byte) ~UPDATE_NEEDED;
 	}
 
 	/**
@@ -563,22 +587,51 @@
 	 *
 	 * @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>
 	 * One of the indicators that the file has been modified by an application
@@ -692,7 +745,8 @@
 	@SuppressWarnings("nls")
 	@Override
 	public String toString() {
-		return getFileMode() + " " + getLength() + " " + getLastModified()
+		return getFileMode() + " " + getLength() + " "
+				+ getLastModifiedInstant()
 				+ " " + getObjectId() + " " + getStage() + " "
 				+ getPathString() + "\n";
 	}
@@ -750,12 +804,25 @@
 		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;
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/errors/IncorrectObjectTypeException.java b/org.eclipse.jgit/src/org/eclipse/jgit/errors/IncorrectObjectTypeException.java
index 5abd0c3..15fd803 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/errors/IncorrectObjectTypeException.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/errors/IncorrectObjectTypeException.java
@@ -63,7 +63,7 @@
 	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 @@
 	}
 
 	/**
-	 * 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.
 	 *
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/JGitText.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/JGitText.java
index 572f963..320036c 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/JGitText.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/JGitText.java
@@ -166,6 +166,7 @@
 	/***/ 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 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 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 String tagAlreadyExists;
 	/***/ public String tagNameInvalid;
 	/***/ public String tagOnRepoWithoutHEADCurrentlyNotSupported;
+	/***/ public String timeoutMeasureFsTimestampResolution;
 	/***/ public String transactionAborted;
 	/***/ public String theFactoryMustNotBeNull;
 	/***/ public String threadInterruptedWhileRunning;
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/ketch/KetchReplica.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/ketch/KetchReplica.java
index a0176d7..0e8377d 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/ketch/KetchReplica.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/ketch/KetchReplica.java
@@ -345,7 +345,7 @@
 	}
 
 	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 @@
 				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));
 				}
 			}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/ketch/LagCheck.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/ketch/LagCheck.java
index c09d872..53fd198 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/ketch/LagCheck.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/ketch/LagCheck.java
@@ -106,7 +106,7 @@
 			return UNKNOWN;
 		}
 
-		if (AnyObjectId.equals(remoteId, ObjectId.zeroId())) {
+		if (AnyObjectId.isEqual(remoteId, ObjectId.zeroId())) {
 			// Replica does not have the txnAccepted reference.
 			return LAGGING;
 		}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/ketch/RemoteGitReplica.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/ketch/RemoteGitReplica.java
index 3c9b187..4bed575 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/ketch/RemoteGitReplica.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/ketch/RemoteGitReplica.java
@@ -200,7 +200,7 @@
 	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;
 		}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/ketch/StageBuilder.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/ketch/StageBuilder.java
index ae82dce..815984d 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/ketch/StageBuilder.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/ketch/StageBuilder.java
@@ -138,7 +138,7 @@
 		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));
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsGarbageCollector.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsGarbageCollector.java
index ca11fb9..f10a1d8 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsGarbageCollector.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsGarbageCollector.java
@@ -661,7 +661,7 @@
 	private int objectsBefore() {
 		int cnt = 0;
 		for (DfsPackFile p : packsBefore)
-			cnt += p.getPackDescription().getObjectCount();
+			cnt += (int) p.getPackDescription().getObjectCount();
 		return cnt;
 	}
 
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsPackParser.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsPackParser.java
index 45e3b19..e4c37cb 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsPackParser.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsPackParser.java
@@ -432,7 +432,7 @@
 		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;
 		}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/ReftableBatchRefUpdate.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/ReftableBatchRefUpdate.java
index 47ac4ec..07fd00f 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/ReftableBatchRefUpdate.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/ReftableBatchRefUpdate.java
@@ -252,7 +252,7 @@
 
 	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 @@
 			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;
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/FileSnapshot.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/FileSnapshot.java
index 1de3135..8650ebf 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/FileSnapshot.java
+++ b/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 @@
  * 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 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 @@
 	 * 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 @@
 	 * 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 @@
 		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 @@
 	 * @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 @@
 	 * 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 @@
 	 */
 	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 @@
 
 	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 @@
 	 * 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 @@
 	 * @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 @@
 	 *            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 @@
 	 *             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 @@
 	 *            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 @@
 	/** {@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 @@
 		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 @@
 		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 boolean isModified(long currLastModified) {
+	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(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 @@
 		// 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;
 	}
 }
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/GC.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/GC.java
index 4540860..08bb6cb 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/GC.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/GC.java
@@ -371,8 +371,9 @@
 					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 @@
 					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))
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/LockFile.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/LockFile.java
index a4fc1a2..fa8732d 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/LockFile.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/LockFile.java
@@ -56,8 +56,12 @@
 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 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);
 		}
 	}
@@ -452,12 +463,23 @@
 	 * 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.
 	 *
 	 * @return get the {@link FileSnapshot} just before commit.
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/ObjectDirectoryPackParser.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/ObjectDirectoryPackParser.java
index ade7a8e..7d31673 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/ObjectDirectoryPackParser.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/ObjectDirectoryPackParser.java
@@ -356,7 +356,7 @@
 		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;
 		}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackFile.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackFile.java
index a89e2ec..88e05af 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackFile.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackFile.java
@@ -60,6 +60,7 @@
 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 @@
 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 @@
 
 	private int activeCopyRawData;
 
-	int packLastModified;
+	Instant packLastModified;
 
 	private PackFileSnapshot fileSnapshot;
 
@@ -168,7 +173,7 @@
 	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
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/UnpackedObjectCache.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/UnpackedObjectCache.java
index 967754a..ea0d269 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/UnpackedObjectCache.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/UnpackedObjectCache.java
@@ -112,7 +112,7 @@
 				if (obj == null)
 					break;
 
-				if (AnyObjectId.equals(obj, toFind))
+				if (AnyObjectId.isEqual(obj, toFind))
 					return true;
 
 				if (++i == ids.length())
@@ -132,7 +132,7 @@
 						continue;
 				}
 
-				if (AnyObjectId.equals(obj, toAdd))
+				if (AnyObjectId.isEqual(obj, toAdd))
 					return true;
 
 				if (++i == ids.length())
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/pack/BinaryDelta.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/pack/BinaryDelta.java
index c7e5ad6..5f69d0a 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/pack/BinaryDelta.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/pack/BinaryDelta.java
@@ -142,7 +142,7 @@
 		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 @@
 		shift = 0;
 		do {
 			c = delta[deltaPtr++] & 0xff;
-			resLen |= ((long) (c & 0x7f)) << shift;
+			resLen |= (c & 0x7f) << shift;
 			shift += 7;
 		} while ((c & 0x80) != 0);
 
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/pack/PackWriter.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/pack/PackWriter.java
index 714e830..6506789 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/pack/PackWriter.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/pack/PackWriter.java
@@ -2198,7 +2198,7 @@
 		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 @@
 			otp.clearReuseAsIs();
 		}
 
-		otp.setDeltaAttempted(reuseDeltas & next.wasDeltaAttempted());
+		otp.setDeltaAttempted(reuseDeltas && next.wasDeltaAttempted());
 		otp.select(next);
 	}
 
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/transport/http/NetscapeCookieFile.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/transport/http/NetscapeCookieFile.java
index 075f55c..e16adb9 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/transport/http/NetscapeCookieFile.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/transport/http/NetscapeCookieFile.java
@@ -78,7 +78,7 @@
  * 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 @@
 
 	/**
 	 * @param path
+	 *            where to find the cookie file
 	 */
 	public NetscapeCookieFile(Path path) {
 		this(path, new Date());
@@ -146,13 +147,17 @@
 	}
 
 	/**
-	 * @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 @@
 	 * @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)
@@ -273,72 +278,18 @@
 	}
 
 	/**
-	 * 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 @@
 
 	}
 
-	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 @@
 	 * @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 @@
 	 * 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
 	 */
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/transport/ssh/OpenSshConfigFile.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/transport/ssh/OpenSshConfigFile.java
index e8a6ba7..c1e94a0 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/transport/ssh/OpenSshConfigFile.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/transport/ssh/OpenSshConfigFile.java
@@ -50,6 +50,7 @@
 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.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 @@
 	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 @@
 	}
 
 	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)) {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/AnyObjectId.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/AnyObjectId.java
index 978dd3a..4f90e69 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/AnyObjectId.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/AnyObjectId.java
@@ -49,6 +49,7 @@
 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 @@
 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 @@
 		// 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 @@
 	 *            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} */
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/CommitBuilder.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/CommitBuilder.java
index 6cbddec..13f71a7 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/CommitBuilder.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/CommitBuilder.java
@@ -57,6 +57,7 @@
 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 @@
 				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 @@
 		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");
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/Config.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/Config.java
index 1032fd0..71f8635 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/Config.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/Config.java
@@ -131,10 +131,11 @@
 	/**
 	 * 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 @@
 				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(' ');
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/ConfigConstants.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/ConfigConstants.java
index 54f6bbc..8f40db6 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/ConfigConstants.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/ConfigConstants.java
@@ -476,4 +476,23 @@
 	 * @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";
 }
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/DefaultTypedConfigGetter.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/DefaultTypedConfigGetter.java
index 4c70d20..e865da8 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/DefaultTypedConfigGetter.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/DefaultTypedConfigGetter.java
@@ -226,6 +226,14 @@
 			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;
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/FileMode.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/FileMode.java
index d4c4d5b..8fa8d5f 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/FileMode.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/FileMode.java
@@ -88,6 +88,7 @@
 	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 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 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 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 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 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 @@
 
 		return new FileMode(bits, Constants.OBJ_BAD) {
 			@Override
+			@SuppressWarnings("NonOverridingEquals")
 			public boolean equals(int a) {
 				return bits == a;
 			}
@@ -206,6 +213,7 @@
 	 *            a int.
 	 * @return true if the mode bits represent the same mode as this object
 	 */
+	@SuppressWarnings("NonOverridingEquals")
 	public abstract boolean equals(int modebits);
 
 	/**
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/IndexDiff.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/IndexDiff.java
index 42d1330..ce1eb59 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/IndexDiff.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/IndexDiff.java
@@ -642,11 +642,12 @@
 	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);
 	}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/ObjectIdSubclassMap.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/ObjectIdSubclassMap.java
index cd57bda..470275b 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/ObjectIdSubclassMap.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/ObjectIdSubclassMap.java
@@ -103,8 +103,9 @@
 		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 @@
 		V obj;
 
 		while ((obj = tbl[i]) != null) {
-			if (AnyObjectId.equals(obj, newValue))
+			if (AnyObjectId.isEqual(obj, newValue))
 				return obj;
 			i = (i + 1) & msk;
 		}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/RefUpdate.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/RefUpdate.java
index 7841627..eca15c0 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/RefUpdate.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/RefUpdate.java
@@ -53,6 +53,7 @@
 import org.eclipse.jgit.revwalk.RevObject;
 import org.eclipse.jgit.revwalk.RevWalk;
 import org.eclipse.jgit.transport.PushCertificate;
+import org.eclipse.jgit.util.References;
 
 /**
  * Creates, updates or deletes any reference.
@@ -753,7 +754,7 @@
 			if (expValue != null) {
 				final ObjectId o;
 				o = oldValue != null ? oldValue : ObjectId.zeroId();
-				if (!AnyObjectId.equals(expValue, o)) {
+				if (!AnyObjectId.isEqual(expValue, o)) {
 					return Result.LOCK_FAILURE;
 				}
 			}
@@ -768,7 +769,8 @@
 			}
 
 			oldObj = safeParseOld(walk, oldValue);
-			if (newObj == oldObj && !detachingSymbolicRef) {
+			if (References.isSameObject(newObj, oldObj)
+					&& !detachingSymbolicRef) {
 				return store.execute(Result.NO_CHANGE);
 			}
 
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/Repository.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/Repository.java
index d53b0c9..68866ea 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/Repository.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/Repository.java
@@ -1536,19 +1536,22 @@
 		final String filePath = file.getPath();
 		final String workDirPath = workDir.getPath();
 
-		if (filePath.length() <= workDirPath.length() ||
-		    filePath.charAt(workDirPath.length()) != File.separatorChar ||
-		    !filePath.startsWith(workDirPath)) {
-			File absWd = workDir.isAbsolute() ? workDir : workDir.getAbsoluteFile();
+		if (filePath.length() <= workDirPath.length()
+				|| filePath.charAt(workDirPath.length()) != File.separatorChar
+				|| !filePath.startsWith(workDirPath)) {
+			File absWd = workDir.isAbsolute() ? workDir
+					: workDir.getAbsoluteFile();
 			File absFile = file.isAbsolute() ? file : file.getAbsoluteFile();
-			if (absWd == workDir && absFile == file)
+			if (absWd.equals(workDir) && absFile.equals(file)) {
 				return ""; //$NON-NLS-1$
+			}
 			return stripWorkDir(absWd, absFile);
 		}
 
 		String relName = filePath.substring(workDirPath.length() + 1);
-		if (File.separatorChar != '/')
+		if (File.separatorChar != '/') {
 			relName = relName.replace(File.separatorChar, '/');
+		}
 		return relName;
 	}
 
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/merge/MergeAlgorithm.java b/org.eclipse.jgit/src/org/eclipse/jgit/merge/MergeAlgorithm.java
index dd42e43..a77cb4f 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/merge/MergeAlgorithm.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/merge/MergeAlgorithm.java
@@ -86,6 +86,11 @@
 	private final static Edit END_EDIT = new Edit(Integer.MAX_VALUE,
 			Integer.MAX_VALUE);
 
+	@SuppressWarnings("ReferenceEquality")
+	private static boolean isEndEdit(Edit edit) {
+		return edit == END_EDIT;
+	}
+
 	/**
 	 * Does the three way merge between a common base and two sequences.
 	 *
@@ -145,7 +150,7 @@
 		// iterate over all edits from base to ours and from base to theirs
 		// leave the loop when there are no edits more for ours or for theirs
 		// (or both)
-		while (theirsEdit != END_EDIT || oursEdit != END_EDIT) {
+		while (!isEndEdit(theirsEdit) || !isEndEdit(oursEdit)) {
 			if (oursEdit.getEndA() < theirsEdit.getBeginA()) {
 				// something was changed in ours not overlapping with any change
 				// from theirs. First add the common part in front of the edit
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/merge/ResolveMerger.java b/org.eclipse.jgit/src/org/eclipse/jgit/merge/ResolveMerger.java
index 0c3d3fe..0b423fb 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/merge/ResolveMerger.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/merge/ResolveMerger.java
@@ -47,6 +47,7 @@
 package org.eclipse.jgit.merge;
 
 import static java.nio.charset.StandardCharsets.UTF_8;
+import static java.time.Instant.EPOCH;
 import static org.eclipse.jgit.diff.DiffAlgorithm.SupportedAlgorithm.HISTOGRAM;
 import static org.eclipse.jgit.lib.ConfigConstants.CONFIG_DIFF_SECTION;
 import static org.eclipse.jgit.lib.ConfigConstants.CONFIG_KEY_ALGORITHM;
@@ -59,6 +60,7 @@
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.OutputStream;
+import java.time.Instant;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
@@ -464,7 +466,7 @@
 	 * @return the entry which was added to the index
 	 */
 	private DirCacheEntry add(byte[] path, CanonicalTreeParser p, int stage,
-			long lastMod, long len) {
+			Instant lastMod, long len) {
 		if (p != null && !p.getEntryFileMode().equals(FileMode.TREE)) {
 			DirCacheEntry e = new DirCacheEntry(path, stage);
 			e.setFileMode(p.getEntryFileMode());
@@ -491,7 +493,7 @@
 				e.getStage());
 		newEntry.setFileMode(e.getFileMode());
 		newEntry.setObjectId(e.getObjectId());
-		newEntry.setLastModified(e.getLastModified());
+		newEntry.setLastModified(e.getLastModifiedInstant());
 		newEntry.setLength(e.getLength());
 		builder.add(newEntry);
 		return newEntry;
@@ -667,16 +669,17 @@
 						// we know about length and lastMod only after we have written the new content.
 						// This will happen later. Set these values to 0 for know.
 						DirCacheEntry e = add(tw.getRawPath(), theirs,
-								DirCacheEntry.STAGE_0, 0, 0);
+								DirCacheEntry.STAGE_0, EPOCH, 0);
 						addToCheckout(tw.getPathString(), e, attributes);
 					}
 					return true;
 				} else {
 					// FileModes are not mergeable. We found a conflict on modes.
 					// For conflicting entries we don't know lastModified and length.
-					add(tw.getRawPath(), base, DirCacheEntry.STAGE_1, 0, 0);
-					add(tw.getRawPath(), ours, DirCacheEntry.STAGE_2, 0, 0);
-					add(tw.getRawPath(), theirs, DirCacheEntry.STAGE_3, 0, 0);
+					add(tw.getRawPath(), base, DirCacheEntry.STAGE_1, EPOCH, 0);
+					add(tw.getRawPath(), ours, DirCacheEntry.STAGE_2, EPOCH, 0);
+					add(tw.getRawPath(), theirs, DirCacheEntry.STAGE_3, EPOCH,
+							0);
 					unmergedPaths.add(tw.getPathString());
 					mergeResults.put(
 							tw.getPathString(),
@@ -708,7 +711,7 @@
 				// the new content.
 				// This will happen later. Set these values to 0 for know.
 				DirCacheEntry e = add(tw.getRawPath(), theirs,
-						DirCacheEntry.STAGE_0, 0, 0);
+						DirCacheEntry.STAGE_0, EPOCH, 0);
 				if (e != null) {
 					addToCheckout(tw.getPathString(), e, attributes);
 				}
@@ -737,16 +740,16 @@
 			// detected later
 			if (nonTree(modeO) && !nonTree(modeT)) {
 				if (nonTree(modeB))
-					add(tw.getRawPath(), base, DirCacheEntry.STAGE_1, 0, 0);
-				add(tw.getRawPath(), ours, DirCacheEntry.STAGE_2, 0, 0);
+					add(tw.getRawPath(), base, DirCacheEntry.STAGE_1, EPOCH, 0);
+				add(tw.getRawPath(), ours, DirCacheEntry.STAGE_2, EPOCH, 0);
 				unmergedPaths.add(tw.getPathString());
 				enterSubtree = false;
 				return true;
 			}
 			if (nonTree(modeT) && !nonTree(modeO)) {
 				if (nonTree(modeB))
-					add(tw.getRawPath(), base, DirCacheEntry.STAGE_1, 0, 0);
-				add(tw.getRawPath(), theirs, DirCacheEntry.STAGE_3, 0, 0);
+					add(tw.getRawPath(), base, DirCacheEntry.STAGE_1, EPOCH, 0);
+				add(tw.getRawPath(), theirs, DirCacheEntry.STAGE_3, EPOCH, 0);
 				unmergedPaths.add(tw.getPathString());
 				enterSubtree = false;
 				return true;
@@ -773,9 +776,9 @@
 			boolean gitlinkConflict = isGitLink(modeO) || isGitLink(modeT);
 			// Don't attempt to resolve submodule link conflicts
 			if (gitlinkConflict || !attributes.canBeContentMerged()) {
-				add(tw.getRawPath(), base, DirCacheEntry.STAGE_1, 0, 0);
-				add(tw.getRawPath(), ours, DirCacheEntry.STAGE_2, 0, 0);
-				add(tw.getRawPath(), theirs, DirCacheEntry.STAGE_3, 0, 0);
+				add(tw.getRawPath(), base, DirCacheEntry.STAGE_1, EPOCH, 0);
+				add(tw.getRawPath(), ours, DirCacheEntry.STAGE_2, EPOCH, 0);
+				add(tw.getRawPath(), theirs, DirCacheEntry.STAGE_3, EPOCH, 0);
 
 				if (gitlinkConflict) {
 					MergeResult<SubmoduleConflict> result = new MergeResult<>(
@@ -822,10 +825,10 @@
 				MergeResult<RawText> result = contentMerge(base, ours, theirs,
 						attributes);
 
-				add(tw.getRawPath(), base, DirCacheEntry.STAGE_1, 0, 0);
-				add(tw.getRawPath(), ours, DirCacheEntry.STAGE_2, 0, 0);
+				add(tw.getRawPath(), base, DirCacheEntry.STAGE_1, EPOCH, 0);
+				add(tw.getRawPath(), ours, DirCacheEntry.STAGE_2, EPOCH, 0);
 				DirCacheEntry e = add(tw.getRawPath(), theirs,
-						DirCacheEntry.STAGE_3, 0, 0);
+						DirCacheEntry.STAGE_3, EPOCH, 0);
 
 				// OURS was deleted checkout THEIRS
 				if (modeO == 0) {
@@ -957,9 +960,9 @@
 				// A conflict occurred, the file will contain conflict markers
 				// the index will be populated with the three stages and the
 				// workdir (if used) contains the halfway merged content.
-				add(tw.getRawPath(), base, DirCacheEntry.STAGE_1, 0, 0);
-				add(tw.getRawPath(), ours, DirCacheEntry.STAGE_2, 0, 0);
-				add(tw.getRawPath(), theirs, DirCacheEntry.STAGE_3, 0, 0);
+				add(tw.getRawPath(), base, DirCacheEntry.STAGE_1, EPOCH, 0);
+				add(tw.getRawPath(), ours, DirCacheEntry.STAGE_2, EPOCH, 0);
+				add(tw.getRawPath(), theirs, DirCacheEntry.STAGE_3, EPOCH, 0);
 				mergeResults.put(tw.getPathString(), result);
 				return;
 			}
@@ -976,7 +979,7 @@
 					? FileMode.REGULAR_FILE : FileMode.fromBits(newMode));
 			if (mergedFile != null) {
 				dce.setLastModified(
-						nonNullRepo().getFS().lastModified(mergedFile));
+						nonNullRepo().getFS().lastModifiedInstant(mergedFile));
 				dce.setLength((int) mergedFile.length());
 			}
 			dce.setObjectId(insertMergeResult(rawMerged, attributes));
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/nls/GlobalBundleCache.java b/org.eclipse.jgit/src/org/eclipse/jgit/nls/GlobalBundleCache.java
index 84bf214..b437f63 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/nls/GlobalBundleCache.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/nls/GlobalBundleCache.java
@@ -43,6 +43,7 @@
 
 package org.eclipse.jgit.nls;
 
+import java.lang.reflect.InvocationTargetException;
 import java.util.HashMap;
 import java.util.Locale;
 import java.util.Map;
@@ -92,12 +93,13 @@
 			}
 			TranslationBundle bundle = bundles.get(type);
 			if (bundle == null) {
-				bundle = type.newInstance();
+				bundle = type.getDeclaredConstructor().newInstance();
 				bundle.load(locale);
 				bundles.put(type, bundle);
 			}
 			return (T) bundle;
-		} catch (InstantiationException | IllegalAccessException e) {
+		} catch (InstantiationException | IllegalAccessException
+				| InvocationTargetException | NoSuchMethodException e) {
 			throw new Error(e);
 		}
 	}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/notes/NoteMapMerger.java b/org.eclipse.jgit/src/org/eclipse/jgit/notes/NoteMapMerger.java
index 325ff4f..ba7223b 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/notes/NoteMapMerger.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/notes/NoteMapMerger.java
@@ -295,14 +295,14 @@
 	private static boolean sameNote(Note a, Note b) {
 		if (a == null && b == null)
 			return true;
-		return a != null && b != null && AnyObjectId.equals(a, b);
+		return a != null && b != null && AnyObjectId.isEqual(a, b);
 	}
 
 	private static boolean sameContent(Note a, Note b) {
 		if (a == null && b == null)
 			return true;
 		return a != null && b != null
-				&& AnyObjectId.equals(a.getData(), b.getData());
+				&& AnyObjectId.isEqual(a.getData(), b.getData());
 	}
 
 	private static InMemoryNoteBucket addIfNotNull(InMemoryNoteBucket result,
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/revwalk/FooterLine.java b/org.eclipse.jgit/src/org/eclipse/jgit/revwalk/FooterLine.java
index d6fed66..84b6d2e 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/revwalk/FooterLine.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/revwalk/FooterLine.java
@@ -95,7 +95,7 @@
 		for (int kPtr = 0; kPtr < len;) {
 			byte b = buffer[bPtr++];
 			if ('A' <= b && b <= 'Z')
-				b += 'a' - 'A';
+				b += (byte) ('a' - 'A');
 			if (b != kRaw[kPtr++])
 				return false;
 		}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/revwalk/ObjectWalk.java b/org.eclipse.jgit/src/org/eclipse/jgit/revwalk/ObjectWalk.java
index af6040f..b6c5810 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/revwalk/ObjectWalk.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/revwalk/ObjectWalk.java
@@ -497,7 +497,7 @@
 				continue;
 			}
 			visitationPolicy.visited(o);
-			if ((o.flags & UNINTERESTING) == 0 | boundary) {
+			if ((o.flags & UNINTERESTING) == 0 || boundary) {
 				if (o instanceof RevTree) {
 					// The previous while loop should have exhausted the stack
 					// of trees.
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/revwalk/RevWalk.java b/org.eclipse.jgit/src/org/eclipse/jgit/revwalk/RevWalk.java
index 634ea4a..4aa8325 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/revwalk/RevWalk.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/revwalk/RevWalk.java
@@ -72,6 +72,7 @@
 import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.revwalk.filter.RevFilter;
 import org.eclipse.jgit.treewalk.filter.TreeFilter;
+import org.eclipse.jgit.util.References;
 
 /**
  * Walks a commit graph and produces the matching commits in order.
@@ -435,9 +436,11 @@
 			markStart(tip);
 			markStart(base);
 			RevCommit mergeBase;
-			while ((mergeBase = next()) != null)
-				if (mergeBase == base)
+			while ((mergeBase = next()) != null) {
+				if (References.isSameObject(mergeBase, base)) {
 					return true;
+				}
+			}
 			return false;
 		} finally {
 			filter = oldRF;
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/storage/file/FileBasedConfig.java b/org.eclipse.jgit/src/org/eclipse/jgit/storage/file/FileBasedConfig.java
index fc6f4a3..10b00b7 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/storage/file/FileBasedConfig.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/storage/file/FileBasedConfig.java
@@ -148,12 +148,38 @@
 	 */
 	@Override
 	public void load() throws IOException, ConfigInvalidException {
+		load(true);
+	}
+
+	/**
+	 * Load the configuration as a Git text style configuration file.
+	 * <p>
+	 * If the file does not exist, this configuration is cleared, and thus
+	 * behaves the same as though the file exists, but is empty.
+	 *
+	 * @param useFileSnapshotWithConfig
+	 *            if {@code true} use the FileSnapshot with config, otherwise
+	 *            use it without config
+	 * @throws IOException
+	 *             if IO failed
+	 * @throws ConfigInvalidException
+	 *             if config is invalid
+	 * @since 5.1.9
+	 */
+	public void load(boolean useFileSnapshotWithConfig)
+			throws IOException, ConfigInvalidException {
 		final int maxRetries = 5;
 		int retryDelayMillis = 20;
 		int retries = 0;
 		while (true) {
 			final FileSnapshot oldSnapshot = snapshot;
-			final FileSnapshot newSnapshot = FileSnapshot.save(getFile());
+			final FileSnapshot newSnapshot;
+			if (useFileSnapshotWithConfig) {
+				newSnapshot = FileSnapshot.save(getFile());
+			} else {
+				// don't use config in this snapshot to avoid endless recursion
+				newSnapshot = FileSnapshot.saveNoConfig(getFile());
+			}
 			try {
 				final byte[] in = IO.readFully(getFile());
 				final ObjectId newHash = hash(in);
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/BasePackFetchConnection.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/BasePackFetchConnection.java
index ea8da42..27cc205 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/BasePackFetchConnection.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/BasePackFetchConnection.java
@@ -670,7 +670,7 @@
 				}
 			}
 
-			if (noDone & receivedReady) {
+			if (noDone && receivedReady) {
 				break SEND_HAVES;
 			}
 			if (statelessRPC) {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/NetRC.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/NetRC.java
index 8562376..7dd019b 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/NetRC.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/NetRC.java
@@ -49,6 +49,7 @@
 import java.io.FileInputStream;
 import java.io.IOException;
 import java.io.InputStreamReader;
+import java.time.Instant;
 import java.util.Collection;
 import java.util.HashMap;
 import java.util.Locale;
@@ -126,7 +127,7 @@
 
 	private File netrc;
 
-	private long lastModified;
+	private Instant lastModified;
 
 	private Map<String, NetRCEntry> hosts = new HashMap<>();
 
@@ -190,8 +191,10 @@
 		if (netrc == null)
 			return null;
 
-		if (this.lastModified != this.netrc.lastModified())
+		if (!this.lastModified
+				.equals(FS.DETECTED.lastModifiedInstant(this.netrc))) {
 			parse();
+		}
 
 		NetRCEntry entry = this.hosts.get(host);
 
@@ -212,7 +215,7 @@
 
 	private void parse() {
 		this.hosts.clear();
-		this.lastModified = this.netrc.lastModified();
+		this.lastModified = FS.DETECTED.lastModifiedInstant(this.netrc);
 
 		try (BufferedReader r = new BufferedReader(
 				new InputStreamReader(new FileInputStream(netrc), UTF_8))) {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/PacketLineIn.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/PacketLineIn.java
index 90f1b37..d73e193 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/PacketLineIn.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/PacketLineIn.java
@@ -259,6 +259,7 @@
 	 * @return true if the given string is {@link #DELIM}, otherwise false.
 	 * @since 5.4
 	 */
+	@SuppressWarnings({ "ReferenceEquality", "StringEquality" })
 	public static boolean isDelimiter(String s) {
 		return s == DELIM;
 	}
@@ -293,6 +294,7 @@
 	 * @return true if the given string is {@link #END}, otherwise false.
 	 * @since 5.4
 	 */
+	@SuppressWarnings({ "ReferenceEquality", "StringEquality" })
 	public static boolean isEnd(String s) {
 		return s == END;
 	}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/ReceiveCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/ReceiveCommand.java
index d61aeb0..a9a995c 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/ReceiveCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/ReceiveCommand.java
@@ -429,7 +429,7 @@
 		this.newId = ObjectId.zeroId();
 		this.newSymref = newSymref;
 		this.name = name;
-		if (AnyObjectId.equals(ObjectId.zeroId(), oldId)) {
+		if (AnyObjectId.isEqual(ObjectId.zeroId(), oldId)) {
 			type = Type.CREATE;
 		} else if (newSymref != null) {
 			type = Type.UPDATE;
@@ -468,7 +468,7 @@
 		this.name = name;
 		if (oldSymref == null) {
 			type = Type.CREATE;
-		} else if (!AnyObjectId.equals(ObjectId.zeroId(), newId)) {
+		} else if (!AnyObjectId.isEqual(ObjectId.zeroId(), newId)) {
 			type = Type.UPDATE;
 		} else {
 			type = Type.DELETE;
@@ -750,7 +750,7 @@
 	public void updateType(RevWalk walk) throws IOException {
 		if (typeIsCorrect)
 			return;
-		if (type == Type.UPDATE && !AnyObjectId.equals(oldId, newId)) {
+		if (type == Type.UPDATE && !AnyObjectId.isEqual(oldId, newId)) {
 			RevObject o = walk.parseAny(oldId);
 			RevObject n = walk.parseAny(newId);
 			if (!(o instanceof RevCommit)
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/RefSpec.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/RefSpec.java
index afd3ada..16c6faf 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/RefSpec.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/RefSpec.java
@@ -49,6 +49,7 @@
 import org.eclipse.jgit.internal.JGitText;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.Ref;
+import org.eclipse.jgit.util.References;
 
 /**
  * Describes how refs in one repository copy into another repository.
@@ -585,8 +586,9 @@
 	}
 
 	private static boolean eq(String a, String b) {
-		if (a == b)
+		if (References.isSameObject(a, b)) {
 			return true;
+		}
 		if (a == null || b == null)
 			return false;
 		return a.equals(b);
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/TrackingRefUpdate.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/TrackingRefUpdate.java
index ba2a673..550a9ef 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/TrackingRefUpdate.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/TrackingRefUpdate.java
@@ -175,7 +175,7 @@
 		private RefUpdate.Result decode(ReceiveCommand.Result status) {
 			switch (status) {
 			case OK:
-				if (AnyObjectId.equals(oldObjectId, newObjectId))
+				if (AnyObjectId.isEqual(oldObjectId, newObjectId))
 					return RefUpdate.Result.NO_CHANGE;
 				switch (getType()) {
 				case CREATE:
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/URIish.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/URIish.java
index 34730d3..7ca9cc1 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/URIish.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/URIish.java
@@ -62,6 +62,7 @@
 import org.eclipse.jgit.internal.JGitText;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.util.RawParseUtils;
+import org.eclipse.jgit.util.References;
 import org.eclipse.jgit.util.StringUtils;
 
 /**
@@ -624,8 +625,9 @@
 	}
 
 	private static boolean eq(String a, String b) {
-		if (a == b)
+		if (References.isSameObject(a, b)) {
 			return true;
+		}
 		if (StringUtils.isEmptyOrNull(a) && StringUtils.isEmptyOrNull(b))
 			return true;
 		if (a == null || b == null)
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/WalkFetchConnection.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/WalkFetchConnection.java
index 2bb5814..b289e42 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/WalkFetchConnection.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/WalkFetchConnection.java
@@ -657,7 +657,7 @@
 		}
 
 		ObjectId act = inserter.insert(type, raw);
-		if (!AnyObjectId.equals(id, act)) {
+		if (!AnyObjectId.isEqual(id, act)) {
 			throw new TransportException(MessageFormat.format(
 					JGitText.get().incorrectHashFor, id.name(), act.name(),
 					Constants.typeString(type),
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/transport/WalkPushConnection.java b/org.eclipse.jgit/src/org/eclipse/jgit/transport/WalkPushConnection.java
index 4c75425..d9103f8 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/transport/WalkPushConnection.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/transport/WalkPushConnection.java
@@ -165,7 +165,7 @@
 				continue;
 			}
 
-			if (AnyObjectId.equals(ObjectId.zeroId(), u.getNewObjectId()))
+			if (AnyObjectId.isEqual(ObjectId.zeroId(), u.getNewObjectId()))
 				deleteCommand(u);
 			else
 				updates.add(u);
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/FileTreeIterator.java b/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/FileTreeIterator.java
index 3d25c23..d432c94 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/FileTreeIterator.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/FileTreeIterator.java
@@ -53,6 +53,7 @@
 import java.io.FileInputStream;
 import java.io.IOException;
 import java.io.InputStream;
+import java.time.Instant;
 
 import org.eclipse.jgit.dircache.DirCacheIterator;
 import org.eclipse.jgit.errors.IncorrectObjectTypeException;
@@ -406,8 +407,14 @@
 		}
 
 		@Override
+		@Deprecated
 		public long getLastModified() {
-			return attributes.getLastModifiedTime();
+			return attributes.getLastModifiedInstant().toEpochMilli();
+		}
+
+		@Override
+		public Instant getLastModifiedInstant() {
+			return attributes.getLastModifiedInstant();
 		}
 
 		@Override
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/WorkingTreeIterator.java b/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/WorkingTreeIterator.java
index 3efa664..f816ff3 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/WorkingTreeIterator.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/WorkingTreeIterator.java
@@ -59,6 +59,7 @@
 import java.nio.charset.CharacterCodingException;
 import java.nio.charset.CharsetEncoder;
 import java.text.MessageFormat;
+import java.time.Instant;
 import java.util.Arrays;
 import java.util.Collections;
 import java.util.Comparator;
@@ -646,12 +647,24 @@
 	 *
 	 * @return last modified time of this file, in milliseconds since the epoch
 	 *         (Jan 1, 1970 UTC).
+	 * @deprecated use {@link #getEntryLastModifiedInstant()} instead
 	 */
+	@Deprecated
 	public long getEntryLastModified() {
 		return current().getLastModified();
 	}
 
 	/**
+	 * Get the last modified time of this entry.
+	 *
+	 * @return last modified time of this file
+	 * @since 5.1.9
+	 */
+	public Instant getEntryLastModifiedInstant() {
+		return current().getLastModifiedInstant();
+	}
+
+	/**
 	 * Obtain an input stream to read the file content.
 	 * <p>
 	 * Efficient implementations are not required. The caller will usually
@@ -921,30 +934,28 @@
 
 		// Git under windows only stores seconds so we round the timestamp
 		// Java gives us if it looks like the timestamp in index is seconds
-		// only. Otherwise we compare the timestamp at millisecond precision,
+		// only. Otherwise we compare the timestamp at nanosecond precision,
 		// unless core.checkstat is set to "minimal", in which case we only
 		// compare the whole second part.
-		long cacheLastModified = entry.getLastModified();
-		long fileLastModified = getEntryLastModified();
-		long lastModifiedMillis = fileLastModified % 1000;
-		long cacheMillis = cacheLastModified % 1000;
-		if (getOptions().getCheckStat() == CheckStat.MINIMAL) {
-			fileLastModified = fileLastModified - lastModifiedMillis;
-			cacheLastModified = cacheLastModified - cacheMillis;
-		} else if (cacheMillis == 0)
-			fileLastModified = fileLastModified - lastModifiedMillis;
-		// Some Java version on Linux return whole seconds only even when
-		// the file systems supports more precision.
-		else if (lastModifiedMillis == 0)
-			cacheLastModified = cacheLastModified - cacheMillis;
-
-		if (fileLastModified != cacheLastModified)
+		Instant cacheLastModified = entry.getLastModifiedInstant();
+		Instant fileLastModified = getEntryLastModifiedInstant();
+		if ((getOptions().getCheckStat() == CheckStat.MINIMAL)
+				|| (cacheLastModified.getNano() == 0)
+				// Some Java version on Linux return whole seconds only even
+				// when the file systems supports more precision.
+				|| (fileLastModified.getNano() == 0)) {
+			if (fileLastModified.getEpochSecond() != cacheLastModified
+					.getEpochSecond()) {
+				return MetadataDiff.DIFFER_BY_TIMESTAMP;
+			}
+		}
+		if (!fileLastModified.equals(cacheLastModified)) {
 			return MetadataDiff.DIFFER_BY_TIMESTAMP;
-		else if (!entry.isSmudged())
-			// The file is clean when you look at timestamps.
-			return MetadataDiff.EQUAL;
-		else
+		} else if (entry.isSmudged()) {
 			return MetadataDiff.SMUDGED;
+		}
+		// The file is clean when when comparing timestamps
+		return MetadataDiff.EQUAL;
 	}
 
 	/**
@@ -1271,10 +1282,26 @@
 		 * instance member instead.
 		 *
 		 * @return time since the epoch (in ms) of the last change.
+		 * @deprecated use {@link #getLastModifiedInstant()} instead
 		 */
+		@Deprecated
 		public abstract long getLastModified();
 
 		/**
+		 * Get the last modified time of this entry.
+		 * <p>
+		 * <b>Note: Efficient implementation required.</b>
+		 * <p>
+		 * The implementation of this method must be efficient. If a subclass
+		 * needs to compute the value they should cache the reference within an
+		 * instance member instead.
+		 *
+		 * @return time of the last change.
+		 * @since 5.1.9
+		 */
+		public abstract Instant getLastModifiedInstant();
+
+		/**
 		 * Get the name of this entry within its directory.
 		 * <p>
 		 * Efficient implementations are not required. The caller will obtain
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/filter/TreeFilterMarker.java b/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/filter/TreeFilterMarker.java
index 738ccbd..c28f035 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/filter/TreeFilterMarker.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/filter/TreeFilterMarker.java
@@ -113,7 +113,7 @@
 				try {
 					boolean marked = filter.include(walk);
 					if (marked)
-						marks |= (1L << index);
+						marks |= (1 << index);
 				} catch (StopWalkException e) {
 					// Don't check tree filter anymore, it will no longer
 					// match
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/util/FS.java b/org.eclipse.jgit/src/org/eclipse/jgit/util/FS.java
index bde750b..421bf81 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/util/FS.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/util/FS.java
@@ -44,6 +44,7 @@
 package org.eclipse.jgit.util;
 
 import static java.nio.charset.StandardCharsets.UTF_8;
+import static java.time.Instant.EPOCH;
 
 import java.io.BufferedReader;
 import java.io.ByteArrayInputStream;
@@ -53,7 +54,9 @@
 import java.io.InputStream;
 import java.io.InputStreamReader;
 import java.io.OutputStream;
+import java.io.OutputStreamWriter;
 import java.io.PrintStream;
+import java.io.Writer;
 import java.nio.charset.Charset;
 import java.nio.file.AccessDeniedException;
 import java.nio.file.FileStore;
@@ -65,27 +68,39 @@
 import java.security.PrivilegedAction;
 import java.text.MessageFormat;
 import java.time.Duration;
+import java.time.Instant;
+import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.HashMap;
 import java.util.Map;
 import java.util.Objects;
 import java.util.Optional;
 import java.util.UUID;
+import java.util.concurrent.CancellationException;
+import java.util.concurrent.CompletableFuture;
 import java.util.concurrent.ConcurrentHashMap;
+import java.util.concurrent.ExecutionException;
 import java.util.concurrent.ExecutorService;
 import java.util.concurrent.Executors;
 import java.util.concurrent.TimeUnit;
+import java.util.concurrent.TimeoutException;
 import java.util.concurrent.atomic.AtomicBoolean;
 import java.util.concurrent.atomic.AtomicReference;
-import java.util.stream.Collectors;
+import java.util.concurrent.locks.Lock;
+import java.util.concurrent.locks.ReentrantLock;
 
 import org.eclipse.jgit.annotations.NonNull;
 import org.eclipse.jgit.annotations.Nullable;
 import org.eclipse.jgit.api.errors.JGitInternalException;
 import org.eclipse.jgit.errors.CommandFailedException;
+import org.eclipse.jgit.errors.ConfigInvalidException;
+import org.eclipse.jgit.errors.LockFailedException;
 import org.eclipse.jgit.internal.JGitText;
+import org.eclipse.jgit.internal.storage.file.FileSnapshot;
+import org.eclipse.jgit.lib.ConfigConstants;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.Repository;
+import org.eclipse.jgit.storage.file.FileBasedConfig;
 import org.eclipse.jgit.treewalk.FileTreeIterator.FileEntry;
 import org.eclipse.jgit.treewalk.FileTreeIterator.FileModeStrategy;
 import org.eclipse.jgit.treewalk.WorkingTreeIterator.Entry;
@@ -188,81 +203,478 @@
 		}
 	}
 
-	private static final class FileStoreAttributeCache {
+	/**
+	 * Attributes of FileStores on this system
+	 *
+	 * @since 5.1.9
+	 */
+	public final static class FileStoreAttributes {
+
+		private static final Duration UNDEFINED_DURATION = Duration
+				.ofNanos(Long.MAX_VALUE);
+
 		/**
-		 * The last modified time granularity of FAT filesystems is 2 seconds.
+		 * Fallback filesystem timestamp resolution. The worst case timestamp
+		 * resolution on FAT filesystems is 2 seconds.
 		 */
-		private static final Duration FALLBACK_TIMESTAMP_RESOLUTION = Duration
+		public static final Duration FALLBACK_TIMESTAMP_RESOLUTION = Duration
 				.ofMillis(2000);
 
-		private static final Map<FileStore, FileStoreAttributeCache> attributeCache = new ConcurrentHashMap<>();
+		/**
+		 * Fallback FileStore attributes used when we can't measure the
+		 * filesystem timestamp resolution. The last modified time granularity
+		 * of FAT filesystems is 2 seconds.
+		 */
+		public static final FileStoreAttributes FALLBACK_FILESTORE_ATTRIBUTES = new FileStoreAttributes(
+				FALLBACK_TIMESTAMP_RESOLUTION);
 
-		static Duration getFsTimestampResolution(Path file) {
+		private static final Map<FileStore, FileStoreAttributes> attributeCache = new ConcurrentHashMap<>();
+
+		private static final SimpleLruCache<Path, FileStoreAttributes> attrCacheByPath = new SimpleLruCache<>(
+				100, 0.2f);
+
+		private static AtomicBoolean background = new AtomicBoolean();
+
+		private static Map<FileStore, Lock> locks = new ConcurrentHashMap<>();
+
+		private static void setBackground(boolean async) {
+			background.set(async);
+		}
+
+		private static final String javaVersionPrefix = System
+				.getProperty("java.vendor") + '|' //$NON-NLS-1$
+				+ System.getProperty("java.version") + '|'; //$NON-NLS-1$
+
+		private static final Duration FALLBACK_MIN_RACY_INTERVAL = Duration
+				.ofMillis(10);
+
+		/**
+		 * Configures size and purge factor of the path-based cache for file
+		 * system attributes. Caching of file system attributes avoids recurring
+		 * lookup of @{code FileStore} of files which may be expensive on some
+		 * platforms.
+		 *
+		 * @param maxSize
+		 *            maximum size of the cache, default is 100
+		 * @param purgeFactor
+		 *            when the size of the map reaches maxSize the oldest
+		 *            entries will be purged to free up some space for new
+		 *            entries, {@code purgeFactor} is the fraction of
+		 *            {@code maxSize} to purge when this happens
+		 * @since 5.1.9
+		 */
+		public static void configureAttributesPathCache(int maxSize,
+				float purgeFactor) {
+			FileStoreAttributes.attrCacheByPath.configure(maxSize, purgeFactor);
+		}
+
+		/**
+		 * Get the FileStoreAttributes for the given FileStore
+		 *
+		 * @param path
+		 *            file residing in the FileStore to get attributes for
+		 * @return FileStoreAttributes for the given path.
+		 */
+		public static FileStoreAttributes get(Path path) {
+			path = path.toAbsolutePath();
+			Path dir = Files.isDirectory(path) ? path : path.getParent();
+			FileStoreAttributes cached = attrCacheByPath.get(dir);
+			if (cached != null) {
+				return cached;
+			}
+			FileStoreAttributes attrs = getFileStoreAttributes(dir);
+			attrCacheByPath.put(dir, attrs);
+			return attrs;
+		}
+
+		private static FileStoreAttributes getFileStoreAttributes(Path dir) {
+			FileStore s;
 			try {
-				Path dir = Files.isDirectory(file) ? file : file.getParent();
-				if (!dir.toFile().canWrite()) {
-					// can not determine FileStore of an unborn directory or in
-					// a read-only directory
-					return FALLBACK_TIMESTAMP_RESOLUTION;
-				}
-				FileStore s = Files.getFileStore(dir);
-				FileStoreAttributeCache c = attributeCache.get(s);
-				if (c == null) {
-					c = new FileStoreAttributeCache(dir);
-					attributeCache.put(s, c);
-					if (LOG.isDebugEnabled()) {
-						LOG.debug(c.toString());
+				if (Files.exists(dir)) {
+					s = Files.getFileStore(dir);
+					FileStoreAttributes c = attributeCache.get(s);
+					if (c != null) {
+						return c;
 					}
+					if (!Files.isWritable(dir)) {
+						// cannot measure resolution in a read-only directory
+						LOG.debug(
+								"{}: cannot measure timestamp resolution in read-only directory {}", //$NON-NLS-1$
+								Thread.currentThread(), dir);
+						return FALLBACK_FILESTORE_ATTRIBUTES;
+					}
+				} else {
+					// cannot determine FileStore of an unborn directory
+					LOG.debug(
+							"{}: cannot measure timestamp resolution of unborn directory {}", //$NON-NLS-1$
+							Thread.currentThread(), dir);
+					return FALLBACK_FILESTORE_ATTRIBUTES;
 				}
-				return c.getFsTimestampResolution();
 
-			} catch (IOException | InterruptedException e) {
-				LOG.warn(e.getMessage(), e);
-				return FALLBACK_TIMESTAMP_RESOLUTION;
+				CompletableFuture<Optional<FileStoreAttributes>> f = CompletableFuture
+						.supplyAsync(() -> {
+							Lock lock = locks.computeIfAbsent(s,
+									l -> new ReentrantLock());
+							if (!lock.tryLock()) {
+								LOG.debug(
+										"{}: couldn't get lock to measure timestamp resolution in {}", //$NON-NLS-1$
+										Thread.currentThread(), dir);
+								return Optional.empty();
+							}
+							Optional<FileStoreAttributes> attributes = Optional
+									.empty();
+							try {
+								// Some earlier future might have set the value
+								// and removed itself since we checked for the
+								// value above. Hence check cache again.
+								FileStoreAttributes c = attributeCache
+										.get(s);
+								if (c != null) {
+									return Optional.of(c);
+								}
+								attributes = readFromConfig(s);
+								if (attributes.isPresent()) {
+									attributeCache.put(s, attributes.get());
+									return attributes;
+								}
+
+								Optional<Duration> resolution = measureFsTimestampResolution(
+										s, dir);
+								if (resolution.isPresent()) {
+									c = new FileStoreAttributes(
+											resolution.get());
+									attributeCache.put(s, c);
+									// for high timestamp resolution measure
+									// minimal racy interval
+									if (c.fsTimestampResolution
+											.toNanos() < 100_000_000L) {
+										c.minimalRacyInterval = measureMinimalRacyInterval(
+												dir);
+									}
+									if (LOG.isDebugEnabled()) {
+										LOG.debug(c.toString());
+									}
+									saveToConfig(s, c);
+								}
+								attributes = Optional.of(c);
+							} finally {
+								lock.unlock();
+								locks.remove(s);
+							}
+							return attributes;
+						});
+				f = f.exceptionally(e -> {
+					LOG.error(e.getLocalizedMessage(), e);
+					return Optional.empty();
+				});
+				// even if measuring in background wait a little - if the result
+				// arrives, it's better than returning the large fallback
+				Optional<FileStoreAttributes> d = background.get() ? f.get(
+						100, TimeUnit.MILLISECONDS) : f.get();
+				if (d.isPresent()) {
+					return d.get();
+				}
+				// return fallback until measurement is finished
+			} catch (IOException | InterruptedException
+					| ExecutionException | CancellationException e) {
+				LOG.error(e.getMessage(), e);
+			} catch (TimeoutException | SecurityException e) {
+				// use fallback
+			}
+			LOG.debug("{}: use fallback timestamp resolution for directory {}", //$NON-NLS-1$
+					Thread.currentThread(), dir);
+			return FALLBACK_FILESTORE_ATTRIBUTES;
+		}
+
+		@SuppressWarnings("boxing")
+		private static Duration measureMinimalRacyInterval(Path dir) {
+			LOG.debug("{}: start measure minimal racy interval in {}", //$NON-NLS-1$
+					Thread.currentThread(), dir);
+			int n = 0;
+			int failures = 0;
+			long racyNanos = 0;
+			ArrayList<Long> deltas = new ArrayList<>();
+			Path probe = dir.resolve(".probe-" + UUID.randomUUID()); //$NON-NLS-1$
+			Instant end = Instant.now().plusSeconds(3);
+			try {
+				Files.createFile(probe);
+				do {
+					n++;
+					write(probe, "a"); //$NON-NLS-1$
+					FileSnapshot snapshot = FileSnapshot.save(probe.toFile());
+					read(probe);
+					write(probe, "b"); //$NON-NLS-1$
+					if (!snapshot.isModified(probe.toFile())) {
+						deltas.add(Long.valueOf(snapshot.lastDelta()));
+						racyNanos = snapshot.lastRacyThreshold();
+						failures++;
+					}
+				} while (Instant.now().compareTo(end) < 0);
+			} catch (IOException e) {
+				LOG.error(e.getMessage(), e);
+				return FALLBACK_MIN_RACY_INTERVAL;
+			} finally {
+				deleteProbe(probe);
+			}
+			if (failures > 0) {
+				Stats stats = new Stats();
+				for (Long d : deltas) {
+					stats.add(d);
+				}
+				LOG.debug(
+						"delta [ns] since modification FileSnapshot failed to detect\n" //$NON-NLS-1$
+								+ "count, failures, racy limit [ns], delta min [ns]," //$NON-NLS-1$
+								+ " delta max [ns], delta avg [ns]," //$NON-NLS-1$
+								+ " delta stddev [ns]\n" //$NON-NLS-1$
+								+ "{}, {}, {}, {}, {}, {}, {}", //$NON-NLS-1$
+						n, failures, racyNanos, stats.min(), stats.max(),
+						stats.avg(), stats.stddev());
+				return Duration
+						.ofNanos(Double.valueOf(stats.max()).longValue());
+			}
+			// since no failures occurred using the measured filesystem
+			// timestamp resolution there is no need for minimal racy interval
+			LOG.debug("{}: no failures when measuring minimal racy interval", //$NON-NLS-1$
+					Thread.currentThread());
+			return Duration.ZERO;
+		}
+
+		private static void write(Path p, String body) throws IOException {
+			FileUtils.mkdirs(p.getParent().toFile(), true);
+			try (Writer w = new OutputStreamWriter(Files.newOutputStream(p),
+					UTF_8)) {
+				w.write(body);
 			}
 		}
 
-		private Duration fsTimestampResolution;
+		private static String read(Path p) throws IOException {
+			final byte[] body = IO.readFully(p.toFile());
+			return new String(body, 0, body.length, UTF_8);
+		}
 
-		Duration getFsTimestampResolution() {
+		private static Optional<Duration> measureFsTimestampResolution(
+			FileStore s, Path dir) {
+			LOG.debug("{}: start measure timestamp resolution {} in {}", //$NON-NLS-1$
+					Thread.currentThread(), s, dir);
+			Path probe = dir.resolve(".probe-" + UUID.randomUUID()); //$NON-NLS-1$
+			try {
+				Files.createFile(probe);
+				FileTime t1 = Files.getLastModifiedTime(probe);
+				FileTime t2 = t1;
+				Instant t1i = t1.toInstant();
+				for (long i = 1; t2.compareTo(t1) <= 0; i += 1 + i / 20) {
+					Files.setLastModifiedTime(probe,
+							FileTime.from(t1i.plusNanos(i * 1000)));
+					t2 = Files.getLastModifiedTime(probe);
+				}
+				Duration fsResolution = Duration.between(t1.toInstant(), t2.toInstant());
+				Duration clockResolution = measureClockResolution();
+				fsResolution = fsResolution.plus(clockResolution);
+				LOG.debug("{}: end measure timestamp resolution {} in {}", //$NON-NLS-1$
+						Thread.currentThread(), s, dir);
+				return Optional.of(fsResolution);
+			} catch (AccessDeniedException e) {
+				LOG.warn(e.getLocalizedMessage(), e); // see bug 548648
+			} catch (IOException e) {
+				LOG.error(e.getLocalizedMessage(), e);
+			} finally {
+				deleteProbe(probe);
+			}
+			return Optional.empty();
+		}
+
+		private static Duration measureClockResolution() {
+			Duration clockResolution = Duration.ZERO;
+			for (int i = 0; i < 10; i++) {
+				Instant t1 = Instant.now();
+				Instant t2 = t1;
+				while (t2.compareTo(t1) <= 0) {
+					t2 = Instant.now();
+				}
+				Duration r = Duration.between(t1, t2);
+				if (r.compareTo(clockResolution) > 0) {
+					clockResolution = r;
+				}
+			}
+			return clockResolution;
+		}
+
+		private static void deleteProbe(Path probe) {
+			try {
+				FileUtils.delete(probe.toFile(),
+						FileUtils.SKIP_MISSING | FileUtils.RETRY);
+			} catch (IOException e) {
+				LOG.error(e.getMessage(), e);
+			}
+		}
+
+		private static Optional<FileStoreAttributes> readFromConfig(
+				FileStore s) {
+			FileBasedConfig userConfig = SystemReader.getInstance()
+					.openUserConfig(null, FS.DETECTED);
+			try {
+				userConfig.load(false);
+			} catch (IOException e) {
+				LOG.error(MessageFormat.format(JGitText.get().readConfigFailed,
+						userConfig.getFile().getAbsolutePath()), e);
+			} catch (ConfigInvalidException e) {
+				LOG.error(MessageFormat.format(
+						JGitText.get().repositoryConfigFileInvalid,
+						userConfig.getFile().getAbsolutePath(),
+						e.getMessage()));
+			}
+			String key = getConfigKey(s);
+			Duration resolution = Duration.ofNanos(userConfig.getTimeUnit(
+					ConfigConstants.CONFIG_FILESYSTEM_SECTION, key,
+					ConfigConstants.CONFIG_KEY_TIMESTAMP_RESOLUTION,
+					UNDEFINED_DURATION.toNanos(), TimeUnit.NANOSECONDS));
+			if (UNDEFINED_DURATION.equals(resolution)) {
+				return Optional.empty();
+			}
+			Duration minRacyThreshold = Duration.ofNanos(userConfig.getTimeUnit(
+					ConfigConstants.CONFIG_FILESYSTEM_SECTION, key,
+					ConfigConstants.CONFIG_KEY_MIN_RACY_THRESHOLD,
+					UNDEFINED_DURATION.toNanos(), TimeUnit.NANOSECONDS));
+			FileStoreAttributes c = new FileStoreAttributes(resolution);
+			if (!UNDEFINED_DURATION.equals(minRacyThreshold)) {
+				c.minimalRacyInterval = minRacyThreshold;
+			}
+			return Optional.of(c);
+		}
+
+		private static void saveToConfig(FileStore s,
+				FileStoreAttributes c) {
+			FileBasedConfig userConfig = SystemReader.getInstance()
+					.openUserConfig(null, FS.DETECTED);
+			long resolution = c.getFsTimestampResolution().toNanos();
+			TimeUnit resolutionUnit = getUnit(resolution);
+			long resolutionValue = resolutionUnit.convert(resolution,
+					TimeUnit.NANOSECONDS);
+
+			long minRacyThreshold = c.getMinimalRacyInterval().toNanos();
+			TimeUnit minRacyThresholdUnit = getUnit(minRacyThreshold);
+			long minRacyThresholdValue = minRacyThresholdUnit
+					.convert(minRacyThreshold, TimeUnit.NANOSECONDS);
+
+			final int max_retries = 5;
+			int retries = 0;
+			boolean succeeded = false;
+			String key = getConfigKey(s);
+			while (!succeeded && retries < max_retries) {
+				try {
+					userConfig.load(false);
+					userConfig.setString(
+							ConfigConstants.CONFIG_FILESYSTEM_SECTION, key,
+							ConfigConstants.CONFIG_KEY_TIMESTAMP_RESOLUTION,
+							String.format("%d %s", //$NON-NLS-1$
+									Long.valueOf(resolutionValue),
+									resolutionUnit.name().toLowerCase()));
+					userConfig.setString(
+							ConfigConstants.CONFIG_FILESYSTEM_SECTION, key,
+							ConfigConstants.CONFIG_KEY_MIN_RACY_THRESHOLD,
+							String.format("%d %s", //$NON-NLS-1$
+									Long.valueOf(minRacyThresholdValue),
+									minRacyThresholdUnit.name().toLowerCase()));
+					userConfig.save();
+					succeeded = true;
+				} catch (LockFailedException e) {
+					// race with another thread, wait a bit and try again
+					try {
+						LOG.warn(MessageFormat.format(JGitText.get().cannotLock,
+								userConfig.getFile().getAbsolutePath()));
+						retries++;
+						Thread.sleep(20);
+					} catch (InterruptedException e1) {
+						Thread.interrupted();
+					}
+				} catch (IOException e) {
+					LOG.error(MessageFormat.format(
+							JGitText.get().cannotSaveConfig,
+							userConfig.getFile().getAbsolutePath()), e);
+				} catch (ConfigInvalidException e) {
+					LOG.error(MessageFormat.format(
+							JGitText.get().repositoryConfigFileInvalid,
+							userConfig.getFile().getAbsolutePath(),
+							e.getMessage()));
+				}
+			}
+		}
+
+		private static String getConfigKey(FileStore s) {
+			final String storeKey;
+			if (SystemReader.getInstance().isWindows()) {
+				Object attribute = null;
+				try {
+					attribute = s.getAttribute("volume:vsn"); //$NON-NLS-1$
+				} catch (IOException ignored) {
+					// ignore
+				}
+				if (attribute instanceof Integer) {
+					storeKey = attribute.toString();
+				} else {
+					storeKey = s.name();
+				}
+			} else {
+				storeKey = s.name();
+			}
+			return javaVersionPrefix + storeKey;
+		}
+
+		private static TimeUnit getUnit(long nanos) {
+			TimeUnit unit;
+			if (nanos < 200_000L) {
+				unit = TimeUnit.NANOSECONDS;
+			} else if (nanos < 200_000_000L) {
+				unit = TimeUnit.MICROSECONDS;
+			} else {
+				unit = TimeUnit.MILLISECONDS;
+			}
+			return unit;
+		}
+
+		private final @NonNull Duration fsTimestampResolution;
+
+		private Duration minimalRacyInterval;
+
+		/**
+		 * @return the measured minimal interval after a file has been modified
+		 *         in which we cannot rely on lastModified to detect
+		 *         modifications
+		 */
+		public Duration getMinimalRacyInterval() {
+			return minimalRacyInterval;
+		}
+
+		/**
+		 * @return the measured filesystem timestamp resolution
+		 */
+		@NonNull
+		public Duration getFsTimestampResolution() {
 			return fsTimestampResolution;
 		}
 
-		private FileStoreAttributeCache(Path dir)
-				throws IOException, InterruptedException {
-			Path probe = dir.resolve(".probe-" + UUID.randomUUID()); //$NON-NLS-1$
-			Files.createFile(probe);
-			try {
-				FileTime startTime = Files.getLastModifiedTime(probe);
-				FileTime actTime = startTime;
-				long sleepTime = 512;
-				while (actTime.compareTo(startTime) <= 0) {
-					TimeUnit.NANOSECONDS.sleep(sleepTime);
-					FileUtils.touch(probe);
-					actTime = Files.getLastModifiedTime(probe);
-					// limit sleep time to max. 100ms
-					if (sleepTime < 100_000_000L) {
-						sleepTime = sleepTime * 2;
-					}
-				}
-				fsTimestampResolution = Duration.between(startTime.toInstant(),
-						actTime.toInstant());
-			} catch (AccessDeniedException e) {
-				LOG.error(e.getLocalizedMessage(), e);
-			} finally {
-				Files.delete(probe);
-			}
+		/**
+		 * Construct a FileStoreAttributeCache entry for the given filesystem
+		 * timestamp resolution
+		 *
+		 * @param fsTimestampResolution
+		 */
+		public FileStoreAttributes(
+				@NonNull Duration fsTimestampResolution) {
+			this.fsTimestampResolution = fsTimestampResolution;
+			this.minimalRacyInterval = Duration.ZERO;
 		}
 
-		@SuppressWarnings("nls")
+		@SuppressWarnings({ "nls", "boxing" })
 		@Override
 		public String toString() {
-			return "FileStoreAttributeCache[" + attributeCache.keySet()
-					.stream()
-					.map(key -> "FileStore[" + key + "]: fsTimestampResolution="
-							+ attributeCache.get(key).getFsTimestampResolution())
-					.collect(Collectors.joining(",\n")) + "]";
+			return String.format(
+					"FileStoreAttributes[fsTimestampResolution=%,d µs, "
+							+ "minimalRacyInterval=%,d µs]",
+					fsTimestampResolution.toNanos() / 1000,
+					minimalRacyInterval.toNanos() / 1000);
 		}
+
 	}
 
 	/** The auto-detected implementation selected for this operating system and JRE. */
@@ -280,6 +692,19 @@
 	}
 
 	/**
+	 * Whether FileStore attributes should be determined asynchronously
+	 *
+	 * @param asynch
+	 *            whether FileStore attributes should be determined
+	 *            asynchronously. If false access to cached attributes may block
+	 *            for some seconds for the first call per FileStore
+	 * @since 5.1.9
+	 */
+	public static void setAsyncFileStoreAttributes(boolean asynch) {
+		FileStoreAttributes.setBackground(asynch);
+	}
+
+	/**
 	 * Auto-detect the appropriate file system abstraction, taking into account
 	 * the presence of a Cygwin installation on the system. Using jgit in
 	 * combination with Cygwin requires a more elaborate (and possibly slower)
@@ -307,18 +732,18 @@
 	}
 
 	/**
-	 * Get an estimate for the filesystem timestamp resolution from a cache of
-	 * timestamp resolution per FileStore, if not yet available it is measured
-	 * for a probe file under the given directory.
+	 * Get cached FileStore attributes, if not yet available measure them using
+	 * a probe file under the given directory.
 	 *
 	 * @param dir
 	 *            the directory under which the probe file will be created to
 	 *            measure the timer resolution.
 	 * @return measured filesystem timestamp resolution
-	 * @since 5.2.3
+	 * @since 5.1.9
 	 */
-	public static Duration getFsTimerResolution(@NonNull Path dir) {
-		return FileStoreAttributeCache.getFsTimestampResolution(dir);
+	public static FileStoreAttributes getFileStoreAttributes(
+			@NonNull Path dir) {
+		return FileStoreAttributes.get(dir);
 	}
 
 	private volatile Holder<File> userHome;
@@ -432,12 +857,42 @@
 	 * @return last modified time of f
 	 * @throws java.io.IOException
 	 * @since 3.0
+	 * @deprecated use {@link #lastModifiedInstant(Path)} instead
 	 */
+	@Deprecated
 	public long lastModified(File f) throws IOException {
 		return FileUtils.lastModified(f);
 	}
 
 	/**
+	 * Get the last modified time of a file system object. If the OS/JRE support
+	 * symbolic links, the modification time of the link is returned, rather
+	 * than that of the link target.
+	 *
+	 * @param p
+	 *            a {@link Path} object.
+	 * @return last modified time of p
+	 * @since 5.1.9
+	 */
+	public Instant lastModifiedInstant(Path p) {
+		return FileUtils.lastModifiedInstant(p);
+	}
+
+	/**
+	 * Get the last modified time of a file system object. If the OS/JRE support
+	 * symbolic links, the modification time of the link is returned, rather
+	 * than that of the link target.
+	 *
+	 * @param f
+	 *            a {@link File} object.
+	 * @return last modified time of p
+	 * @since 5.1.9
+	 */
+	public Instant lastModifiedInstant(File f) {
+		return FileUtils.lastModifiedInstant(f.toPath());
+	}
+
+	/**
 	 * Set the last modified time of a file system object. If the OS/JRE support
 	 * symbolic links, the link is modified, not the target,
 	 *
@@ -447,12 +902,29 @@
 	 *            last modified time
 	 * @throws java.io.IOException
 	 * @since 3.0
+	 * @deprecated use {@link #setLastModified(Path, Instant)} instead
 	 */
+	@Deprecated
 	public void setLastModified(File f, long time) throws IOException {
 		FileUtils.setLastModified(f, time);
 	}
 
 	/**
+	 * Set the last modified time of a file system object. If the OS/JRE support
+	 * symbolic links, the link is modified, not the target,
+	 *
+	 * @param p
+	 *            a {@link Path} object.
+	 * @param time
+	 *            last modified time
+	 * @throws java.io.IOException
+	 * @since 5.1.9
+	 */
+	public void setLastModified(Path p, Instant time) throws IOException {
+		FileUtils.setLastModified(p, time);
+	}
+
+	/**
 	 * Get the length of a file or link, If the OS/JRE supports symbolic links
 	 * it's the length of the link, else the length of the target.
 	 *
@@ -1522,9 +1994,19 @@
 		/**
 		 * @return the time (milliseconds since 1970-01-01) when this object was
 		 *         last modified
+		 * @deprecated use getLastModifiedInstant instead
 		 */
+		@Deprecated
 		public long getLastModifiedTime() {
-			return lastModifiedTime;
+			return lastModifiedInstant.toEpochMilli();
+		}
+
+		/**
+		 * @return the time when this object was last modified
+		 * @since 5.1.9
+		 */
+		public Instant getLastModifiedInstant() {
+			return lastModifiedInstant;
 		}
 
 		private final boolean isDirectory;
@@ -1535,7 +2017,7 @@
 
 		private final long creationTime;
 
-		private final long lastModifiedTime;
+		private final Instant lastModifiedInstant;
 
 		private final boolean isExecutable;
 
@@ -1553,7 +2035,7 @@
 		Attributes(FS fs, File file, boolean exists, boolean isDirectory,
 				boolean isExecutable, boolean isSymbolicLink,
 				boolean isRegularFile, long creationTime,
-				long lastModifiedTime, long length) {
+				Instant lastModifiedInstant, long length) {
 			this.fs = fs;
 			this.file = file;
 			this.exists = exists;
@@ -1562,7 +2044,7 @@
 			this.isSymbolicLink = isSymbolicLink;
 			this.isRegularFile = isRegularFile;
 			this.creationTime = creationTime;
-			this.lastModifiedTime = lastModifiedTime;
+			this.lastModifiedInstant = lastModifiedInstant;
 			this.length = length;
 		}
 
@@ -1574,7 +2056,7 @@
 		 * @param path
 		 */
 		public Attributes(File path, FS fs) {
-			this(fs, path, false, false, false, false, false, 0L, 0L, 0L);
+			this(fs, path, false, false, false, false, false, 0L, EPOCH, 0L);
 		}
 
 		/**
@@ -1620,7 +2102,7 @@
 		boolean exists = isDirectory || isFile;
 		boolean canExecute = exists && !isDirectory && canExecute(path);
 		boolean isSymlink = false;
-		long lastModified = exists ? path.lastModified() : 0L;
+		Instant lastModified = exists ? lastModifiedInstant(path) : EPOCH;
 		long createTime = 0L;
 		return new Attributes(this, path, exists, isDirectory, canExecute,
 				isSymlink, isFile, createTime, lastModified, -1);
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/util/FS_POSIX.java b/org.eclipse.jgit/src/org/eclipse/jgit/util/FS_POSIX.java
index faef9fd..6ec50c2 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/util/FS_POSIX.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/util/FS_POSIX.java
@@ -396,7 +396,12 @@
 		}
 		Path lockPath = lock.toPath();
 		Path link = null;
-		FileStore store = Files.getFileStore(lockPath);
+		FileStore store = null;
+		try {
+			store = Files.getFileStore(lockPath);
+		} catch (SecurityException e) {
+			return true;
+		}
 		try {
 			Boolean canLink = CAN_HARD_LINK.computeIfAbsent(store,
 					s -> Boolean.TRUE);
@@ -462,7 +467,12 @@
 		}
 		Path link = null;
 		Path path = file.toPath();
-		FileStore store = Files.getFileStore(path);
+		FileStore store = null;
+		try {
+			store = Files.getFileStore(path);
+		} catch (SecurityException e) {
+			return token(true, null);
+		}
 		try {
 			Boolean canLink = CAN_HARD_LINK.computeIfAbsent(store,
 					s -> Boolean.TRUE);
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/util/FS_Win32.java b/org.eclipse.jgit/src/org/eclipse/jgit/util/FS_Win32.java
index 3ccbd72..7fe80bb 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/util/FS_Win32.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/util/FS_Win32.java
@@ -149,7 +149,7 @@
 									attrs.isSymbolicLink(),
 									attrs.isRegularFile(),
 									attrs.creationTime().toMillis(),
-									attrs.lastModifiedTime().toMillis(),
+									attrs.lastModifiedTime().toInstant(),
 									attrs.size());
 							result.add(new FileEntry(f, fs, attributes,
 									fileModeStrategy));
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/util/FileUtils.java b/org.eclipse.jgit/src/org/eclipse/jgit/util/FileUtils.java
index 0e8732d..4a773b0 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/util/FileUtils.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/util/FileUtils.java
@@ -50,7 +50,7 @@
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.IOException;
-import java.io.OutputStream;
+import java.nio.channels.FileChannel;
 import java.nio.file.AtomicMoveNotSupportedException;
 import java.nio.file.CopyOption;
 import java.nio.file.Files;
@@ -58,6 +58,7 @@
 import java.nio.file.LinkOption;
 import java.nio.file.Path;
 import java.nio.file.StandardCopyOption;
+import java.nio.file.StandardOpenOption;
 import java.nio.file.attribute.BasicFileAttributeView;
 import java.nio.file.attribute.BasicFileAttributes;
 import java.nio.file.attribute.FileTime;
@@ -67,6 +68,7 @@
 import java.text.MessageFormat;
 import java.text.Normalizer;
 import java.text.Normalizer.Form;
+import java.time.Instant;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Locale;
@@ -75,11 +77,14 @@
 import org.eclipse.jgit.internal.JGitText;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.util.FS.Attributes;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 /**
  * File Utilities
  */
 public class FileUtils {
+	private static final Logger LOG = LoggerFactory.getLogger(FileUtils.class);
 
 	/**
 	 * Option to delete given {@code File}
@@ -674,13 +679,32 @@
 	 * @return lastModified attribute for given file, not following symbolic
 	 *         links
 	 * @throws IOException
+	 * @deprecated use {@link #lastModifiedInstant(Path)} instead which returns
+	 *             FileTime
 	 */
+	@Deprecated
 	static long lastModified(File file) throws IOException {
 		return Files.getLastModifiedTime(toPath(file), LinkOption.NOFOLLOW_LINKS)
 				.toMillis();
 	}
 
 	/**
+	 * @param path
+	 * @return lastModified attribute for given file, not following symbolic
+	 *         links
+	 */
+	static Instant lastModifiedInstant(Path path) {
+		try {
+			return Files.getLastModifiedTime(path, LinkOption.NOFOLLOW_LINKS)
+					.toInstant();
+		} catch (IOException e) {
+			LOG.error(MessageFormat
+					.format(JGitText.get().readLastModifiedFailed, path));
+			return Instant.ofEpochMilli(path.toFile().lastModified());
+		}
+	}
+
+	/**
 	 * Return all the attributes of a file, without following symbolic links.
 	 *
 	 * @param file
@@ -698,11 +722,22 @@
 	 * @param time
 	 * @throws IOException
 	 */
+	@Deprecated
 	static void setLastModified(File file, long time) throws IOException {
 		Files.setLastModifiedTime(toPath(file), FileTime.fromMillis(time));
 	}
 
 	/**
+	 * @param path
+	 * @param time
+	 * @throws IOException
+	 */
+	static void setLastModified(Path path, Instant time)
+			throws IOException {
+		Files.setLastModifiedTime(path, FileTime.from(time));
+	}
+
+	/**
 	 * @param file
 	 * @return {@code true} if the given file exists, not following symbolic
 	 *         links
@@ -806,7 +841,7 @@
 					readAttributes.isSymbolicLink(),
 					readAttributes.isRegularFile(), //
 					readAttributes.creationTime().toMillis(), //
-					readAttributes.lastModifiedTime().toMillis(),
+					readAttributes.lastModifiedTime().toInstant(),
 					readAttributes.isSymbolicLink() ? Constants
 							.encode(readSymLink(file)).length
 							: readAttributes.size());
@@ -845,7 +880,7 @@
 					readAttributes.isSymbolicLink(),
 					readAttributes.isRegularFile(), //
 					readAttributes.creationTime().toMillis(), //
-					readAttributes.lastModifiedTime().toMillis(),
+					readAttributes.lastModifiedTime().toInstant(),
 					readAttributes.size());
 			return attributes;
 		} catch (IOException e) {
@@ -936,11 +971,13 @@
 	 * @param f
 	 *            the file to touch
 	 * @throws IOException
-	 * @since 5.2.3
+	 * @since 5.1.8
 	 */
 	public static void touch(Path f) throws IOException {
-		try (OutputStream fos = Files.newOutputStream(f)) {
-			// touch the file
+		try (FileChannel fc = FileChannel.open(f, StandardOpenOption.CREATE,
+				StandardOpenOption.APPEND, StandardOpenOption.SYNC)) {
+			// touch
 		}
+		Files.setLastModifiedTime(f, FileTime.from(Instant.now()));
 	}
 }
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/util/GitDateParser.java b/org.eclipse.jgit/src/org/eclipse/jgit/util/GitDateParser.java
index a339b9a..56a1731 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/util/GitDateParser.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/util/GitDateParser.java
@@ -126,7 +126,7 @@
 		DEFAULT("EEE MMM dd HH:mm:ss yyyy Z"), // //$NON-NLS-1$
 		LOCAL("EEE MMM dd HH:mm:ss yyyy"); //$NON-NLS-1$
 
-		String formatStr;
+		private final String formatStr;
 
 		private ParseableSimpleDateFormat(String formatStr) {
 			this.formatStr = formatStr;
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/util/RefMap.java b/org.eclipse.jgit/src/org/eclipse/jgit/util/RefMap.java
index d7a4c25..9663e3c 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/util/RefMap.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/util/RefMap.java
@@ -443,8 +443,10 @@
 					if (r.getName().equals(ref.getName())) {
 						final ObjectId a = r.getObjectId();
 						final ObjectId b = ref.getObjectId();
-						if (a != null && b != null && AnyObjectId.equals(a, b))
+						if (a != null && b != null
+								&& AnyObjectId.isEqual(a, b)) {
 							return true;
+						}
 					}
 				}
 			}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/util/References.java b/org.eclipse.jgit/src/org/eclipse/jgit/util/References.java
new file mode 100644
index 0000000..341fbfa
--- /dev/null
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/util/References.java
@@ -0,0 +1,67 @@
+/*
+ * 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;
+
+/**
+ * Utility methods for object references
+ *
+ * @since 5.4
+ */
+public interface References {
+
+	/**
+	 * Compare two references
+	 *
+	 * @param <T>
+	 *            type of the references
+	 * @param ref1
+	 *            first reference
+	 * @param ref2
+	 *            second reference
+	 * @return {@code true} if both references refer to the same object
+	 */
+	@SuppressWarnings("ReferenceEquality")
+	public static <T> boolean isSameObject(T ref1, T ref2) {
+		return ref1 == ref2;
+	}
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/util/SimpleLruCache.java b/org.eclipse.jgit/src/org/eclipse/jgit/util/SimpleLruCache.java
new file mode 100644
index 0000000..7235b15
--- /dev/null
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/util/SimpleLruCache.java
@@ -0,0 +1,255 @@
+/*
+ * Copyright (C) 2019, Marc Strapetz <marc.strapetz@syntevo.com>
+ * 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 java.text.MessageFormat;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.List;
+import java.util.Map;
+import java.util.concurrent.ConcurrentHashMap;
+import java.util.concurrent.locks.Lock;
+import java.util.concurrent.locks.ReentrantLock;
+
+import org.eclipse.jgit.annotations.NonNull;
+import org.eclipse.jgit.internal.JGitText;
+
+/**
+ * Simple limited size cache based on ConcurrentHashMap purging entries in LRU
+ * order when reaching size limit
+ *
+ * @param <K>
+ *            the type of keys maintained by this cache
+ * @param <V>
+ *            the type of mapped values
+ *
+ * @since 5.1.9
+ */
+public class SimpleLruCache<K, V> {
+
+	private static class Entry<K, V> {
+
+		private final K key;
+
+		private final V value;
+
+		// pseudo clock timestamp of the last access to this entry
+		private volatile long lastAccessed;
+
+		private long lastAccessedSorting;
+
+		Entry(K key, V value, long lastAccessed) {
+			this.key = key;
+			this.value = value;
+			this.lastAccessed = lastAccessed;
+		}
+
+		void copyAccessTime() {
+			lastAccessedSorting = lastAccessed;
+		}
+
+		@SuppressWarnings("nls")
+		@Override
+		public String toString() {
+			return "Entry [lastAccessed=" + lastAccessed + ", key=" + key
+					+ ", value=" + value + "]";
+		}
+	}
+
+	private Lock lock = new ReentrantLock();
+
+	private Map<K, Entry<K,V>> map = new ConcurrentHashMap<>();
+
+	private volatile int maximumSize;
+
+	private int purgeSize;
+
+	// pseudo clock to implement LRU order of access to entries
+	private volatile long time = 0L;
+
+	private static void checkPurgeFactor(float purgeFactor) {
+		if (purgeFactor <= 0 || purgeFactor >= 1) {
+			throw new IllegalArgumentException(
+					MessageFormat.format(JGitText.get().invalidPurgeFactor,
+							Float.valueOf(purgeFactor)));
+		}
+	}
+
+	private static int purgeSize(int maxSize, float purgeFactor) {
+		return (int) ((1 - purgeFactor) * maxSize);
+	}
+
+	/**
+	 * Create a new cache
+	 *
+	 * @param maxSize
+	 *            maximum size of the cache, to reduce need for synchronization
+	 *            this is not a hard limit. The real size of the cache could be
+	 *            slightly above this maximum if multiple threads put new values
+	 *            concurrently
+	 * @param purgeFactor
+	 *            when the size of the map reaches maxSize the oldest entries
+	 *            will be purged to free up some space for new entries,
+	 *            {@code purgeFactor} is the fraction of {@code maxSize} to
+	 *            purge when this happens
+	 */
+	public SimpleLruCache(int maxSize, float purgeFactor) {
+		checkPurgeFactor(purgeFactor);
+		this.maximumSize = maxSize;
+		this.purgeSize = purgeSize(maxSize, purgeFactor);
+	}
+
+	/**
+	 * Returns the value to which the specified key is mapped, or {@code null}
+	 * if this map contains no mapping for the key.
+	 *
+	 * <p>
+	 * More formally, if this cache contains a mapping from a key {@code k} to a
+	 * value {@code v} such that {@code key.equals(k)}, then this method returns
+	 * {@code v}; otherwise it returns {@code null}. (There can be at most one
+	 * such mapping.)
+	 *
+	 * @param key
+	 *            the key
+	 *
+	 * @throws NullPointerException
+	 *             if the specified key is null
+	 *
+	 * @return value mapped for this key, or {@code null} if no value is mapped
+	 */
+	@SuppressWarnings("NonAtomicVolatileUpdate")
+	public V get(Object key) {
+		Entry<K, V> entry = map.get(key);
+		if (entry != null) {
+			entry.lastAccessed = ++time;
+			return entry.value;
+		}
+		return null;
+	}
+
+	/**
+	 * Maps the specified key to the specified value in this cache. Neither the
+	 * key nor the value can be null.
+	 *
+	 * <p>
+	 * The value can be retrieved by calling the {@code get} method with a key
+	 * that is equal to the original key.
+	 *
+	 * @param key
+	 *            key with which the specified value is to be associated
+	 * @param value
+	 *            value to be associated with the specified key
+	 * @return the previous value associated with {@code key}, or {@code null}
+	 *         if there was no mapping for {@code key}
+	 * @throws NullPointerException
+	 *             if the specified key or value is null
+	 */
+	@SuppressWarnings("NonAtomicVolatileUpdate")
+	public V put(@NonNull K key, @NonNull V value) {
+		map.put(key, new Entry<>(key, value, ++time));
+		if (map.size() > maximumSize) {
+			purge();
+		}
+		return value;
+	}
+
+	/**
+	 * Returns the current size of this cache
+	 *
+	 * @return the number of key-value mappings in this cache
+	 */
+	public int size() {
+		return map.size();
+	}
+
+	/**
+	 * Reconfigures the cache. If {@code maxSize} is reduced some entries will
+	 * be purged.
+	 *
+	 * @param maxSize
+	 *            maximum size of the cache
+	 *
+	 * @param purgeFactor
+	 *            when the size of the map reaches maxSize the oldest entries
+	 *            will be purged to free up some space for new entries,
+	 *            {@code purgeFactor} is the fraction of {@code maxSize} to
+	 *            purge when this happens
+	 */
+	public void configure(int maxSize, float purgeFactor) {
+		lock.lock();
+		try {
+			checkPurgeFactor(purgeFactor);
+			this.maximumSize = maxSize;
+			this.purgeSize = purgeSize(maxSize, purgeFactor);
+			if (map.size() >= maximumSize) {
+				purge();
+			}
+		} finally {
+			lock.unlock();
+		}
+	}
+
+	private void purge() {
+		// don't try to compete if another thread already has the lock
+		if (lock.tryLock()) {
+			try {
+				List<Entry> entriesToPurge = new ArrayList<>(map.values());
+				// copy access times to avoid other threads interfere with
+				// sorting
+				for (Entry e : entriesToPurge) {
+					e.copyAccessTime();
+				}
+				Collections.sort(entriesToPurge,
+						Comparator.comparingLong(o -> -o.lastAccessedSorting));
+				for (int index = purgeSize; index < entriesToPurge
+						.size(); index++) {
+					map.remove(entriesToPurge.get(index).key);
+				}
+			} finally {
+				lock.unlock();
+			}
+		}
+	}
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/util/Stats.java b/org.eclipse.jgit/src/org/eclipse/jgit/util/Stats.java
new file mode 100644
index 0000000..e9307d3
--- /dev/null
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/util/Stats.java
@@ -0,0 +1,132 @@
+/*
+ * 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;
+
+/**
+ * Simple double statistics, computed incrementally, variance and standard
+ * deviation using Welford's online algorithm, see
+ * https://en.wikipedia.org/wiki/Algorithms_for_calculating_variance#Welford's_online_algorithm
+ *
+ * @since 5.1.9
+ */
+public class Stats {
+	private int n = 0;
+
+	private double avg = 0.0;
+
+	private double min = 0.0;
+
+	private double max = 0.0;
+
+	private double sum = 0.0;
+
+	/**
+	 * Add a value
+	 *
+	 * @param x
+	 *            value
+	 */
+	public void add(double x) {
+		n++;
+		min = n == 1 ? x : Math.min(min, x);
+		max = n == 1 ? x : Math.max(max, x);
+		double d = x - avg;
+		avg += d / n;
+		sum += d * d * (n - 1) / n;
+	}
+
+	/**
+	 * @return number of the added values
+	 */
+	public int count() {
+		return n;
+	}
+
+	/**
+	 * @return minimum of the added values
+	 */
+	public double min() {
+		if (n < 1) {
+			return Double.NaN;
+		}
+		return min;
+	}
+
+	/**
+	 * @return maximum of the added values
+	 */
+	public double max() {
+		if (n < 1) {
+			return Double.NaN;
+		}
+		return max;
+	}
+
+	/**
+	 * @return average of the added values
+	 */
+
+	public double avg() {
+		if (n < 1) {
+			return Double.NaN;
+		}
+		return avg;
+	}
+
+	/**
+	 * @return variance of the added values
+	 */
+	public double var() {
+		if (n < 2) {
+			return Double.NaN;
+		}
+		return sum / (n - 1);
+	}
+
+	/**
+	 * @return standard deviation of the added values
+	 */
+	public double stddev() {
+		return Math.sqrt(this.var());
+	}
+}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/util/StringUtils.java b/org.eclipse.jgit/src/org/eclipse/jgit/util/StringUtils.java
index 3868e56..f4b6f9d 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/util/StringUtils.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/util/StringUtils.java
@@ -139,8 +139,9 @@
 	 * @return true if a equals b
 	 */
 	public static boolean equalsIgnoreCase(String a, String b) {
-		if (a == b)
+		if (References.isSameObject(a, b)) {
 			return true;
+		}
 		if (a.length() != b.length())
 			return false;
 		for (int i = 0; i < a.length(); i++) {
diff --git a/pom.xml b/pom.xml
index 2ad57b5..8da9a88 100644
--- a/pom.xml
+++ b/pom.xml
@@ -194,7 +194,7 @@
     <osgi-core-version>4.3.1</osgi-core-version>
     <servlet-api-version>3.1.0</servlet-api-version>
     <jetty-version>9.4.14.v20181114</jetty-version>
-    <japicmp-version>0.13.0</japicmp-version>
+    <japicmp-version>0.14.1</japicmp-version>
     <httpclient-version>4.5.6</httpclient-version>
     <httpcore-version>4.4.10</httpcore-version>
     <slf4j-version>1.7.2</slf4j-version>
@@ -204,10 +204,11 @@
     <gson-version>2.8.2</gson-version>
     <bouncycastle-version>1.61</bouncycastle-version>
     <spotbugs-maven-plugin-version>3.1.12.2</spotbugs-maven-plugin-version>
-    <maven-surefire-version>2.22.2</maven-surefire-version>
-    <maven-compiler-plugin-version>3.8.1</maven-compiler-plugin-version>
     <maven-project-info-reports-plugin-version>3.0.0</maven-project-info-reports-plugin-version>
     <maven-jxr-plugin-version>3.0.0</maven-jxr-plugin-version>
+    <maven-surefire-plugin-version>3.0.0-M3</maven-surefire-plugin-version>
+    <maven-surefire-report-plugin-version>${maven-surefire-plugin-version}</maven-surefire-report-plugin-version>
+    <maven-compiler-plugin-version>3.8.1</maven-compiler-plugin-version>
 
     <!-- Properties to enable jacoco code coverage analysis -->
     <sonar.core.codeCoveragePlugin>jacoco</sonar.core.codeCoveragePlugin>
@@ -294,7 +295,7 @@
         <plugin>
           <groupId>org.apache.maven.plugins</groupId>
           <artifactId>maven-surefire-plugin</artifactId>
-          <version>${maven-surefire-version}</version>
+          <version>${maven-surefire-plugin-version}</version>
           <configuration>
             <forkCount>${test-fork-count}</forkCount>
             <reuseForks>true</reuseForks>
@@ -383,7 +384,7 @@
         <plugin>
           <groupId>org.apache.maven.plugins</groupId>
           <artifactId>maven-surefire-report-plugin</artifactId>
-          <version>${maven-surefire-version}</version>
+          <version>${maven-surefire-report-plugin-version}</version>
         </plugin>
         <plugin>
           <groupId>org.apache.maven.plugins</groupId>
@@ -395,7 +396,26 @@
           <artifactId>maven-project-info-reports-plugin</artifactId>
           <version>${maven-project-info-reports-plugin-version}</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-compiler-plugin</artifactId>
+          <version>${maven-compiler-plugin-version}</version>
+        </plugin>
+        <plugin>
+          <groupId>org.apache.maven.plugins</groupId>
+          <artifactId>maven-resources-plugin</artifactId>
+          <version>3.1.0</version>
+        </plugin>
         <plugin>
           <groupId>org.springframework.boot</groupId>
           <artifactId>spring-boot-maven-plugin</artifactId>
@@ -856,7 +876,7 @@
               <dependency>
                 <groupId>org.codehaus.plexus</groupId>
                 <artifactId>plexus-compiler-javac</artifactId>
-                <version>2.8.4</version>
+                <version>2.8.5</version>
               </dependency>
               <dependency>
                 <groupId>org.codehaus.plexus</groupId>
diff --git a/tools/BUILD b/tools/BUILD
index d94ce02..bfe0d6e 100644
--- a/tools/BUILD
+++ b/tools/BUILD
@@ -26,13 +26,13 @@
         "-Xep:ReferenceEquality:WARN",
         "-Xep:StringEquality:WARN",
         "-Xep:WildcardImport:ERROR",
-        "-Xep:AmbiguousMethodReference:WARN",
+        "-Xep:AmbiguousMethodReference:ERROR",
         "-Xep:BadAnnotationImplementation:ERROR",
         "-Xep:BadComparable:WARN",
         "-Xep:BoxedPrimitiveConstructor:ERROR",
         "-Xep:CannotMockFinalClass:ERROR",
         "-Xep:ClassCanBeStatic:ERROR",
-        "-Xep:ClassNewInstance:WARN",
+        "-Xep:ClassNewInstance:ERROR",
         "-Xep:DefaultCharset:ERROR",
         "-Xep:DoubleCheckedLocking:ERROR",
         "-Xep:ElementsCountedInLoop:ERROR",
@@ -47,7 +47,7 @@
         "-Xep:FutureReturnValueIgnored:ERROR",
         "-Xep:GetClassOnEnum:ERROR",
         "-Xep:ImmutableAnnotationChecker:ERROR",
-        "-Xep:ImmutableEnumChecker:WARN",
+        "-Xep:ImmutableEnumChecker:ERROR",
         "-Xep:IncompatibleModifiers:ERROR",
         "-Xep:InjectOnConstructorOfAbstractClass:ERROR",
         "-Xep:InputStreamSlowMultibyteRead:ERROR",
@@ -58,9 +58,9 @@
         "-Xep:MissingFail:ERROR",
         "-Xep:MissingOverride:ERROR",
         "-Xep:MutableConstantField:ERROR",
-        "-Xep:NarrowingCompoundAssignment:WARN",
+        "-Xep:NarrowingCompoundAssignment:ERROR",
         "-Xep:NonAtomicVolatileUpdate:ERROR",
-        "-Xep:NonOverridingEquals:WARN",
+        "-Xep:NonOverridingEquals:ERROR",
         "-Xep:NullableConstructor:ERROR",
         "-Xep:NullablePrimitive:ERROR",
         "-Xep:NullableVoid:ERROR",
@@ -70,7 +70,7 @@
         "-Xep:ProtoFieldPreconditionsCheckNotNull:ERROR",
         "-Xep:ProtocolBufferOrdinal:ERROR",
         "-Xep:RequiredModifiers:ERROR",
-        "-Xep:ShortCircuitBoolean:WARN",
+        "-Xep:ShortCircuitBoolean:ERROR",
         "-Xep:SimpleDateFormatConstant:ERROR",
         "-Xep:StaticGuardedByInstance:ERROR",
         "-Xep:SynchronizeOnNonFinalField:ERROR",