Merge branch 'stable-5.3' into stable-5.4

* stable-5.3:
  Fix NPE in RebaseTodoFile#parseComments
  Fix NPE in ObjectIdOwnerMap#get
  Fix NPE in CommitOnlyTest#getHead
  FileUtils#lastModifiedInstant should not log error if path doesn't exist
  Cache user global and system-wide git configurations
  Avoid setup and saving FileStoreAttributes compete for ~/.gitconfig lock
  Add missing dependencies for running FS_POSIXTest in Eclipse
  Fix javadoc for SystemReader#getInstance
  Improve retry handling when saving FileStoreAttributes fails
  Ensure FSTest uses MockSystemReader
  Make supportsAtomicCreateNewFile return true as default
  Update orbit to R20190602212107-2019-06 to enable backports from master
  Handle InvalidPathException in FS_POSIX#createNewFileAtomic
  Ensure root cause of lock creation failures is logged
  Implement toString in MockSystemReader and MockConfig
  LocalDiskRefTreeDatabaseTest shall use MockSystemReader
  Ensure LocalDiskRepositoryTestCase#setup fully uses MockSystemReader
  Ensure we use MockSystemReader in tests
  Override FileBasedConfig's save method in MockConfig
  Remove FileBasedConfig.load(boolean) introduced in d45219ba
  Disable debug log for FS in org.eclipse.jgit.test
  Bazel: enable logging for tests in org.eclipse.jgit.test
  LockFile: log exception if creation of lock file failed
  Stop using deprecated Constants.CHARACTER_ENCODING

Change-Id: I43c2ab8b44c3e87d48e4072907ad169c81e3ffe0
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>

WORKSPACE

 
 maven_jar(
     name = "mockito",
-    artifact = "org.mockito:mockito-core:2.13.0",
-    sha1 = "8e372943974e4a121fb8617baced8ebfe46d54f0",
+    artifact = "org.mockito:mockito-core:2.23.0",
+    sha1 = "497ddb32fd5d01f9dbe99a2ec790aeb931dff1b1",
 )
 
-BYTE_BUDDY_VERSION = "1.7.9"
+BYTE_BUDDY_VERSION = "1.9.0"
 
 maven_jar(
-    name = "byte_buddy",
+    name = "bytebuddy",
     artifact = "net.bytebuddy:byte-buddy:" + BYTE_BUDDY_VERSION,
-    sha1 = "51218a01a882c04d0aba8c028179cce488bbcb58",
+    sha1 = "8cb0d5baae526c9df46ae17693bbba302640538b",
 )
 
 maven_jar(
-    name = "byte_buddy_agent",
+    name = "bytebuddy-agent",
     artifact = "net.bytebuddy:byte-buddy-agent:" + BYTE_BUDDY_VERSION,
-    sha1 = "a6c65f9da7f467ee1f02ff2841ffd3155aee2fc9",
+    sha1 = "37b5703b4a6290be3fffc63ae9c6bcaaee0ff856",
 )
 
 maven_jar(

lib/BUILD

     testonly = 1,
     visibility = ["//visibility:public"],
     exports = [
+        "@bytebuddy//jar",
+        "@bytebuddy-agent//jar",
         "@hamcrest-core//jar",
         "@hamcrest-library//jar",
         "@junit//jar",
+        "@mockito//jar",
+        "@objenesis//jar"
     ],
 )
 
     testonly = 1,
     visibility = ["//visibility:public"],
     exports = [
-        "@byte_buddy//jar",
-        "@byte_buddy_agent//jar",
+        "@bytebuddy//jar",
+        "@bytebuddy-agent//jar",
         "@mockito//jar",
         "@objenesis//jar",
     ],

org.eclipse.jgit.http.test/tst/org/eclipse/jgit/http/test/SmartClientSmartServerTest.java

 import org.eclipse.jgit.revwalk.RevBlob;
 import org.eclipse.jgit.revwalk.RevCommit;
 import org.eclipse.jgit.revwalk.RevWalk;
-import org.eclipse.jgit.storage.file.FileBasedConfig;
 import org.eclipse.jgit.transport.AbstractAdvertiseRefsHook;
 import org.eclipse.jgit.transport.AdvertiseRefsHook;
 import org.eclipse.jgit.transport.CredentialItem;
 import org.eclipse.jgit.transport.http.HttpConnectionFactory;
 import org.eclipse.jgit.transport.http.JDKHttpConnectionFactory;
 import org.eclipse.jgit.transport.http.apache.HttpClientConnectionFactory;
-import org.eclipse.jgit.util.FS;
 import org.eclipse.jgit.util.HttpSupport;
 import org.eclipse.jgit.util.SystemReader;
 import org.hamcrest.Matchers;
 
 	@Test
 	public void testInitialClone_RedirectMax() throws Exception {
-		FileBasedConfig userConfig = SystemReader.getInstance()
-				.openUserConfig(null, FS.DETECTED);
+		StoredConfig userConfig = SystemReader.getInstance()
+				.getUserConfig();
 		userConfig.setInt("http", null, "maxRedirects", 4);
 		userConfig.save();
 		initialClone_Redirect(4, 302);
 
 	@Test
 	public void testInitialClone_RedirectTooOften() throws Exception {
-		FileBasedConfig userConfig = SystemReader.getInstance()
-				.openUserConfig(null, FS.DETECTED);
+		StoredConfig userConfig = SystemReader.getInstance()
+				.getUserConfig();
 		userConfig.setInt("http", null, "maxRedirects", 3);
 		userConfig.save();
 
 
 	@Test
 	public void testInitialClone_RedirectOnPostAllowed() throws Exception {
-		FileBasedConfig userConfig = SystemReader.getInstance()
-				.openUserConfig(null, FS.DETECTED);
+		StoredConfig userConfig = SystemReader.getInstance()
+				.getUserConfig();
 		userConfig.setString("http", null, "followRedirects", "true");
 		userConfig.save();
 
 
 	@Test
 	public void testInitialClone_RedirectForbidden() throws Exception {
-		FileBasedConfig userConfig = SystemReader.getInstance()
-				.openUserConfig(null, FS.DETECTED);
+		StoredConfig userConfig = SystemReader.getInstance()
+				.getUserConfig();
 		userConfig.setString("http", null, "followRedirects", "false");
 		userConfig.save();
 

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

 		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
+		mockSystemReader = new MockSystemReader();
+		SystemReader.setInstance(mockSystemReader);
+
+		// Measure timer resolution before the test to avoid time critical tests
+		// are affected by time needed for measurement.
+		// The MockSystemReader must be configured first since we need to use
+		// the same one here
 		FS.getFileStoreAttributes(tmp.toPath().getParent());
 
-		mockSystemReader = new MockSystemReader();
-		mockSystemReader.userGitConfig = new FileBasedConfig(new File(tmp,
-				"usergitconfig"), FS.DETECTED);
+		FileBasedConfig userConfig = new FileBasedConfig(
+				new File(tmp, "usergitconfig"), FS.DETECTED);
 		// We have to set autoDetach to false for tests, because tests expect to be able
 		// to clean up by recursively removing the repository, and background GC might be
 		// in the middle of writing or deleting files, which would disrupt this.
-		mockSystemReader.userGitConfig.setBoolean(ConfigConstants.CONFIG_GC_SECTION,
+		userConfig.setBoolean(ConfigConstants.CONFIG_GC_SECTION,
 				null, ConfigConstants.CONFIG_KEY_AUTODETACH, false);
-		mockSystemReader.userGitConfig.save();
+		userConfig.save();
+		mockSystemReader.setUserGitConfig(userConfig);
 		ceilTestDirectories(getCeilings());
-		SystemReader.setInstance(mockSystemReader);
 
 		author = new PersonIdent("J. Author", "jauthor@example.com");
 		committer = new PersonIdent("J. Committer", "jcommitter@example.com");

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

 import org.eclipse.jgit.errors.ConfigInvalidException;
 import org.eclipse.jgit.lib.Config;
 import org.eclipse.jgit.lib.Constants;
+import org.eclipse.jgit.lib.StoredConfig;
 import org.eclipse.jgit.storage.file.FileBasedConfig;
 import org.eclipse.jgit.util.FS;
 import org.eclipse.jgit.util.SystemReader;
 			// Do nothing
 		}
 
+		@Override
+		public void save() throws IOException {
+			// Do nothing
+		}
+
 		@Override
 		public boolean isOutdated() {
 			return false;
 		}
+
+		@Override
+		public String toString() {
+			return "MockConfig";
+		}
 	}
 
 	long now = 1250379778668L; // Sat Aug 15 20:12:58 GMT-03:30 2009
 
 	final Map<String, String> values = new HashMap<>();
 
-	FileBasedConfig userGitConfig;
+	private FileBasedConfig userGitConfig;
 
 	FileBasedConfig systemGitConfig;
 
+	/**
+	 * Set the user-level git config
+	 *
+	 * @param userGitConfig
+	 *            set another user-level git config
+	 * @return the old user-level git config
+	 */
+	public FileBasedConfig setUserGitConfig(FileBasedConfig userGitConfig) {
+		FileBasedConfig old = this.userGitConfig;
+		this.userGitConfig = userGitConfig;
+		return old;
+	}
+
+	/**
+	 * Set the system-level git config
+	 *
+	 * @param systemGitConfig
+	 *            the new system-level git config
+	 * @return the old system-level config
+	 */
+	public FileBasedConfig setSystemGitConfig(FileBasedConfig systemGitConfig) {
+		FileBasedConfig old = this.systemGitConfig;
+		this.systemGitConfig = systemGitConfig;
+		return old;
+	}
+
 	/**
 	 * Constructor for <code>MockSystemReader</code>
 	 */
 		return systemGitConfig;
 	}
 
+	@Override
+	public StoredConfig getUserConfig()
+			throws IOException, ConfigInvalidException {
+		return userGitConfig;
+	}
+
+	@Override
+	public StoredConfig getSystemConfig()
+			throws IOException, ConfigInvalidException {
+		return systemGitConfig;
+	}
+
 	/** {@inheritDoc} */
 	@Override
 	public String getHostname() {
 			e.printStackTrace();
 		}
 	}
+
+	@Override
+	public String toString() {
+		return "MockSystemReader";
+	}
+
 }

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

 import org.apache.http.impl.client.HttpClientBuilder;
 import org.eclipse.jetty.servlet.ServletContextHandler;
 import org.eclipse.jetty.servlet.ServletHolder;
+import org.eclipse.jgit.junit.MockSystemReader;
 import org.eclipse.jgit.junit.http.AppServer;
 import org.eclipse.jgit.lfs.errors.LfsException;
 import org.eclipse.jgit.lfs.lib.AnyLongObjectId;
 import org.eclipse.jgit.util.FS;
 import org.eclipse.jgit.util.FileUtils;
 import org.eclipse.jgit.util.IO;
+import org.eclipse.jgit.util.SystemReader;
 import org.junit.After;
 import org.junit.Before;
 
 
 	@Before
 	public void setup() throws Exception {
+		SystemReader.setInstance(new MockSystemReader());
 		tmp = Files.createTempDirectory("jgit_test_");
 
 		// measure timer resolution before the test to avoid time critical tests

org.eclipse.jgit.lfs/src/org/eclipse/jgit/lfs/InstallBuiltinLfsCommand.java

 package org.eclipse.jgit.lfs;
 
 import java.io.IOException;
-import java.text.MessageFormat;
 
+import org.eclipse.jgit.api.errors.InvalidConfigurationException;
 import org.eclipse.jgit.errors.ConfigInvalidException;
-import org.eclipse.jgit.lfs.internal.LfsText;
 import org.eclipse.jgit.lib.ConfigConstants;
 import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.lib.StoredConfig;
-import org.eclipse.jgit.storage.file.FileBasedConfig;
 import org.eclipse.jgit.util.FS;
 import org.eclipse.jgit.util.LfsFactory.LfsInstallCommand;
 import org.eclipse.jgit.util.SystemReader;
 
 	private Repository repository;
 
-	/** {@inheritDoc} */
+	/**
+	 * {@inheritDoc}
+	 *
+	 * @throws IOException
+	 *             if an I/O error occurs while accessing a git config or
+	 *             executing {@code git lfs install} in an external process
+	 * @throws InvalidConfigurationException
+	 *             if a git configuration is invalid
+	 * @throws InterruptedException
+	 *             if the current thread is interrupted while waiting for the
+	 *             {@code git lfs install} executed in an external process
+	 */
 	@Override
-	public Void call() throws Exception {
+	public Void call() throws IOException, InvalidConfigurationException,
+			InterruptedException {
 		StoredConfig cfg = null;
 		if (repository == null) {
-			cfg = loadUserConfig();
+			try {
+				cfg = SystemReader.getInstance().getUserConfig();
+			} catch (ConfigInvalidException e) {
+				throw new InvalidConfigurationException(e.getMessage(), e);
+			}
 		} else {
 			cfg = repository.getConfig();
 		}
 		return this;
 	}
 
-	private StoredConfig loadUserConfig() throws IOException {
-		FileBasedConfig c = SystemReader.getInstance().openUserConfig(null,
-				FS.DETECTED);
-		try {
-			c.load();
-		} catch (ConfigInvalidException e1) {
-			throw new IOException(MessageFormat
-					.format(LfsText.get().userConfigInvalid, c.getFile()
-							.getAbsolutePath(), e1),
-					e1);
-		}
-
-		return c;
-	}
-
 }

org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.10.target

 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <?pde?>
 <!-- generated with https://github.com/eclipse-cbi/targetplatform-dsl -->
-<target name="jgit-4.10" sequenceNumber="1559548426">
+<target name="jgit-4.10" sequenceNumber="1566251637">
   <locations>
     <location includeMode="slicer" includeAllPlatforms="false" includeSource="true" includeConfigurePhase="true" type="InstallableUnit">
       <unit id="org.eclipse.jetty.client" version="9.4.14.v20181114"/>
       <unit id="javaewah.source" version="1.1.6.v20160919-1400"/>
       <unit id="org.objenesis" version="2.6.0.v20180420-1519"/>
       <unit id="org.objenesis.source" version="2.6.0.v20180420-1519"/>
-      <unit id="org.mockito" version="2.13.0.v20180426-1843"/>
-      <unit id="org.mockito.source" version="2.13.0.v20180426-1843"/>
-      <unit id="net.bytebuddy.byte-buddy" version="1.7.9.v20180420-1519"/>
-      <unit id="net.bytebuddy.byte-buddy.source" version="1.7.9.v20180420-1519"/>
-      <unit id="net.bytebuddy.byte-buddy-agent" version="1.7.9.v20180420-1519"/>
-      <unit id="net.bytebuddy.byte-buddy-agent.source" version="1.7.9.v20180420-1519"/>
+      <unit id="org.mockito" version="2.23.0.v20190527-1420"/>
+      <unit id="org.mockito.source" version="2.23.0.v20190527-1420"/>
+      <unit id="net.bytebuddy.byte-buddy" version="1.9.0.v20181107-1410"/>
+      <unit id="net.bytebuddy.byte-buddy.source" version="1.9.0.v20181107-1410"/>
+      <unit id="net.bytebuddy.byte-buddy-agent" version="1.9.0.v20181106-1534"/>
+      <unit id="net.bytebuddy.byte-buddy-agent.source" version="1.9.0.v20181106-1534"/>
       <unit id="com.google.gson" version="2.8.2.v20180104-1110"/>
       <unit id="com.google.gson.source" version="2.8.2.v20180104-1110"/>
       <unit id="com.jcraft.jsch" version="0.1.55.v20190404-1902"/>

org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.11.target

 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <?pde?>
 <!-- generated with https://github.com/eclipse-cbi/targetplatform-dsl -->
-<target name="jgit-4.11" sequenceNumber="1559548429">
+<target name="jgit-4.11" sequenceNumber="1566251633">
   <locations>
     <location includeMode="slicer" includeAllPlatforms="false" includeSource="true" includeConfigurePhase="true" type="InstallableUnit">
       <unit id="org.eclipse.jetty.client" version="9.4.14.v20181114"/>
       <unit id="javaewah.source" version="1.1.6.v20160919-1400"/>
       <unit id="org.objenesis" version="2.6.0.v20180420-1519"/>
       <unit id="org.objenesis.source" version="2.6.0.v20180420-1519"/>
-      <unit id="org.mockito" version="2.13.0.v20180426-1843"/>
-      <unit id="org.mockito.source" version="2.13.0.v20180426-1843"/>
-      <unit id="net.bytebuddy.byte-buddy" version="1.7.9.v20180420-1519"/>
-      <unit id="net.bytebuddy.byte-buddy.source" version="1.7.9.v20180420-1519"/>
-      <unit id="net.bytebuddy.byte-buddy-agent" version="1.7.9.v20180420-1519"/>
-      <unit id="net.bytebuddy.byte-buddy-agent.source" version="1.7.9.v20180420-1519"/>
+      <unit id="org.mockito" version="2.23.0.v20190527-1420"/>
+      <unit id="org.mockito.source" version="2.23.0.v20190527-1420"/>
+      <unit id="net.bytebuddy.byte-buddy" version="1.9.0.v20181107-1410"/>
+      <unit id="net.bytebuddy.byte-buddy.source" version="1.9.0.v20181107-1410"/>
+      <unit id="net.bytebuddy.byte-buddy-agent" version="1.9.0.v20181106-1534"/>
+      <unit id="net.bytebuddy.byte-buddy-agent.source" version="1.9.0.v20181106-1534"/>
       <unit id="com.google.gson" version="2.8.2.v20180104-1110"/>
       <unit id="com.google.gson.source" version="2.8.2.v20180104-1110"/>
       <unit id="com.jcraft.jsch" version="0.1.55.v20190404-1902"/>

org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.12-staging.target

 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <?pde?>
 <!-- generated with https://github.com/eclipse-cbi/targetplatform-dsl -->
-<target name="jgit-4.12-staging" sequenceNumber="1559548433">
+<target name="jgit-4.12-staging" sequenceNumber="1566251632">
   <locations>
     <location includeMode="slicer" includeAllPlatforms="false" includeSource="true" includeConfigurePhase="true" type="InstallableUnit">
       <unit id="org.eclipse.jetty.client" version="9.4.14.v20181114"/>
       <unit id="javaewah.source" version="1.1.6.v20160919-1400"/>
       <unit id="org.objenesis" version="2.6.0.v20180420-1519"/>
       <unit id="org.objenesis.source" version="2.6.0.v20180420-1519"/>
-      <unit id="org.mockito" version="2.13.0.v20180426-1843"/>
-      <unit id="org.mockito.source" version="2.13.0.v20180426-1843"/>
-      <unit id="net.bytebuddy.byte-buddy" version="1.7.9.v20180420-1519"/>
-      <unit id="net.bytebuddy.byte-buddy.source" version="1.7.9.v20180420-1519"/>
-      <unit id="net.bytebuddy.byte-buddy-agent" version="1.7.9.v20180420-1519"/>
-      <unit id="net.bytebuddy.byte-buddy-agent.source" version="1.7.9.v20180420-1519"/>
+      <unit id="org.mockito" version="2.23.0.v20190527-1420"/>
+      <unit id="org.mockito.source" version="2.23.0.v20190527-1420"/>
+      <unit id="net.bytebuddy.byte-buddy" version="1.9.0.v20181107-1410"/>
+      <unit id="net.bytebuddy.byte-buddy.source" version="1.9.0.v20181107-1410"/>
+      <unit id="net.bytebuddy.byte-buddy-agent" version="1.9.0.v20181106-1534"/>
+      <unit id="net.bytebuddy.byte-buddy-agent.source" version="1.9.0.v20181106-1534"/>
       <unit id="com.google.gson" version="2.8.2.v20180104-1110"/>
       <unit id="com.google.gson.source" version="2.8.2.v20180104-1110"/>
       <unit id="com.jcraft.jsch" version="0.1.55.v20190404-1902"/>

org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.6.target

 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <?pde?>
 <!-- generated with https://github.com/eclipse-cbi/targetplatform-dsl -->
-<target name="jgit-4.6" sequenceNumber="1559548436">
+<target name="jgit-4.6" sequenceNumber="1566251641">
   <locations>
     <location includeMode="slicer" includeAllPlatforms="false" includeSource="true" includeConfigurePhase="true" type="InstallableUnit">
       <unit id="org.eclipse.jetty.client" version="9.4.14.v20181114"/>
       <unit id="javaewah.source" version="1.1.6.v20160919-1400"/>
       <unit id="org.objenesis" version="2.6.0.v20180420-1519"/>
       <unit id="org.objenesis.source" version="2.6.0.v20180420-1519"/>
-      <unit id="org.mockito" version="2.13.0.v20180426-1843"/>
-      <unit id="org.mockito.source" version="2.13.0.v20180426-1843"/>
-      <unit id="net.bytebuddy.byte-buddy" version="1.7.9.v20180420-1519"/>
-      <unit id="net.bytebuddy.byte-buddy.source" version="1.7.9.v20180420-1519"/>
-      <unit id="net.bytebuddy.byte-buddy-agent" version="1.7.9.v20180420-1519"/>
-      <unit id="net.bytebuddy.byte-buddy-agent.source" version="1.7.9.v20180420-1519"/>
+      <unit id="org.mockito" version="2.23.0.v20190527-1420"/>
+      <unit id="org.mockito.source" version="2.23.0.v20190527-1420"/>
+      <unit id="net.bytebuddy.byte-buddy" version="1.9.0.v20181107-1410"/>
+      <unit id="net.bytebuddy.byte-buddy.source" version="1.9.0.v20181107-1410"/>
+      <unit id="net.bytebuddy.byte-buddy-agent" version="1.9.0.v20181106-1534"/>
+      <unit id="net.bytebuddy.byte-buddy-agent.source" version="1.9.0.v20181106-1534"/>
       <unit id="com.google.gson" version="2.8.2.v20180104-1110"/>
       <unit id="com.google.gson.source" version="2.8.2.v20180104-1110"/>
       <unit id="com.jcraft.jsch" version="0.1.55.v20190404-1902"/>

org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.7.target

 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <?pde?>
 <!-- generated with https://github.com/eclipse-cbi/targetplatform-dsl -->
-<target name="jgit-4.7" sequenceNumber="1559548440">
+<target name="jgit-4.7" sequenceNumber="1566251627">
   <locations>
     <location includeMode="slicer" includeAllPlatforms="false" includeSource="true" includeConfigurePhase="true" type="InstallableUnit">
       <unit id="org.eclipse.jetty.client" version="9.4.14.v20181114"/>
       <unit id="javaewah.source" version="1.1.6.v20160919-1400"/>
       <unit id="org.objenesis" version="2.6.0.v20180420-1519"/>
       <unit id="org.objenesis.source" version="2.6.0.v20180420-1519"/>
-      <unit id="org.mockito" version="2.13.0.v20180426-1843"/>
-      <unit id="org.mockito.source" version="2.13.0.v20180426-1843"/>
-      <unit id="net.bytebuddy.byte-buddy" version="1.7.9.v20180420-1519"/>
-      <unit id="net.bytebuddy.byte-buddy.source" version="1.7.9.v20180420-1519"/>
-      <unit id="net.bytebuddy.byte-buddy-agent" version="1.7.9.v20180420-1519"/>
-      <unit id="net.bytebuddy.byte-buddy-agent.source" version="1.7.9.v20180420-1519"/>
+      <unit id="org.mockito" version="2.23.0.v20190527-1420"/>
+      <unit id="org.mockito.source" version="2.23.0.v20190527-1420"/>
+      <unit id="net.bytebuddy.byte-buddy" version="1.9.0.v20181107-1410"/>
+      <unit id="net.bytebuddy.byte-buddy.source" version="1.9.0.v20181107-1410"/>
+      <unit id="net.bytebuddy.byte-buddy-agent" version="1.9.0.v20181106-1534"/>
+      <unit id="net.bytebuddy.byte-buddy-agent.source" version="1.9.0.v20181106-1534"/>
       <unit id="com.google.gson" version="2.8.2.v20180104-1110"/>
       <unit id="com.google.gson.source" version="2.8.2.v20180104-1110"/>
       <unit id="com.jcraft.jsch" version="0.1.55.v20190404-1902"/>

org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.8.target

 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <?pde?>
 <!-- generated with https://github.com/eclipse-cbi/targetplatform-dsl -->
-<target name="jgit-4.8" sequenceNumber="1559548443">
+<target name="jgit-4.8" sequenceNumber="1566251616">
   <locations>
     <location includeMode="slicer" includeAllPlatforms="false" includeSource="true" includeConfigurePhase="true" type="InstallableUnit">
       <unit id="org.eclipse.jetty.client" version="9.4.14.v20181114"/>
       <unit id="javaewah.source" version="1.1.6.v20160919-1400"/>
       <unit id="org.objenesis" version="2.6.0.v20180420-1519"/>
       <unit id="org.objenesis.source" version="2.6.0.v20180420-1519"/>
-      <unit id="org.mockito" version="2.13.0.v20180426-1843"/>
-      <unit id="org.mockito.source" version="2.13.0.v20180426-1843"/>
-      <unit id="net.bytebuddy.byte-buddy" version="1.7.9.v20180420-1519"/>
-      <unit id="net.bytebuddy.byte-buddy.source" version="1.7.9.v20180420-1519"/>
-      <unit id="net.bytebuddy.byte-buddy-agent" version="1.7.9.v20180420-1519"/>
-      <unit id="net.bytebuddy.byte-buddy-agent.source" version="1.7.9.v20180420-1519"/>
+      <unit id="org.mockito" version="2.23.0.v20190527-1420"/>
+      <unit id="org.mockito.source" version="2.23.0.v20190527-1420"/>
+      <unit id="net.bytebuddy.byte-buddy" version="1.9.0.v20181107-1410"/>
+      <unit id="net.bytebuddy.byte-buddy.source" version="1.9.0.v20181107-1410"/>
+      <unit id="net.bytebuddy.byte-buddy-agent" version="1.9.0.v20181106-1534"/>
+      <unit id="net.bytebuddy.byte-buddy-agent.source" version="1.9.0.v20181106-1534"/>
       <unit id="com.google.gson" version="2.8.2.v20180104-1110"/>
       <unit id="com.google.gson.source" version="2.8.2.v20180104-1110"/>
       <unit id="com.jcraft.jsch" version="0.1.55.v20190404-1902"/>

org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.9.target

 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <?pde?>
 <!-- generated with https://github.com/eclipse-cbi/targetplatform-dsl -->
-<target name="jgit-4.9" sequenceNumber="1559548447">
+<target name="jgit-4.9" sequenceNumber="1566251604">
   <locations>
     <location includeMode="slicer" includeAllPlatforms="false" includeSource="true" includeConfigurePhase="true" type="InstallableUnit">
       <unit id="org.eclipse.jetty.client" version="9.4.14.v20181114"/>
       <unit id="javaewah.source" version="1.1.6.v20160919-1400"/>
       <unit id="org.objenesis" version="2.6.0.v20180420-1519"/>
       <unit id="org.objenesis.source" version="2.6.0.v20180420-1519"/>
-      <unit id="org.mockito" version="2.13.0.v20180426-1843"/>
-      <unit id="org.mockito.source" version="2.13.0.v20180426-1843"/>
-      <unit id="net.bytebuddy.byte-buddy" version="1.7.9.v20180420-1519"/>
-      <unit id="net.bytebuddy.byte-buddy.source" version="1.7.9.v20180420-1519"/>
-      <unit id="net.bytebuddy.byte-buddy-agent" version="1.7.9.v20180420-1519"/>
-      <unit id="net.bytebuddy.byte-buddy-agent.source" version="1.7.9.v20180420-1519"/>
+      <unit id="org.mockito" version="2.23.0.v20190527-1420"/>
+      <unit id="org.mockito.source" version="2.23.0.v20190527-1420"/>
+      <unit id="net.bytebuddy.byte-buddy" version="1.9.0.v20181107-1410"/>
+      <unit id="net.bytebuddy.byte-buddy.source" version="1.9.0.v20181107-1410"/>
+      <unit id="net.bytebuddy.byte-buddy-agent" version="1.9.0.v20181106-1534"/>
+      <unit id="net.bytebuddy.byte-buddy-agent.source" version="1.9.0.v20181106-1534"/>
       <unit id="com.google.gson" version="2.8.2.v20180104-1110"/>
       <unit id="com.google.gson.source" version="2.8.2.v20180104-1110"/>
       <unit id="com.jcraft.jsch" version="0.1.55.v20190404-1902"/>

org.eclipse.jgit.packaging/org.eclipse.jgit.target/orbit/R20190602212107-2019-06.tpd

 	javaewah.source [1.1.6.v20160919-1400,1.1.6.v20160919-1400]
 	org.objenesis [2.6.0.v20180420-1519,2.6.0.v20180420-1519]
 	org.objenesis.source [2.6.0.v20180420-1519,2.6.0.v20180420-1519]
-	org.mockito [2.13.0.v20180426-1843,2.13.0.v20180426-1843]
-	org.mockito.source [2.13.0.v20180426-1843,2.13.0.v20180426-1843]
-	net.bytebuddy.byte-buddy [1.7.9.v20180420-1519,1.7.9.v20180420-1519]
-	net.bytebuddy.byte-buddy.source [1.7.9.v20180420-1519,1.7.9.v20180420-1519]
-	net.bytebuddy.byte-buddy-agent [1.7.9.v20180420-1519,1.7.9.v20180420-1519]
-	net.bytebuddy.byte-buddy-agent.source [1.7.9.v20180420-1519,1.7.9.v20180420-1519]
+	org.mockito [2.23.0.v20190527-1420,2.23.0.v20190527-1420]
+	org.mockito.source [2.23.0.v20190527-1420,2.23.0.v20190527-1420]
+	net.bytebuddy.byte-buddy [1.9.0.v20181107-1410,1.9.0.v20181107-1410]
+	net.bytebuddy.byte-buddy.source [1.9.0.v20181107-1410,1.9.0.v20181107-1410]
+	net.bytebuddy.byte-buddy-agent [1.9.0.v20181106-1534,1.9.0.v20181106-1534]
+	net.bytebuddy.byte-buddy-agent.source [1.9.0.v20181106-1534,1.9.0.v20181106-1534]
 	com.google.gson [2.8.2.v20180104-1110,2.8.2.v20180104-1110]
 	com.google.gson.source [2.8.2.v20180104-1110,2.8.2.v20180104-1110]
 	com.jcraft.jsch [0.1.55.v20190404-1902,0.1.55.v20190404-1902]
 	org.apache.sshd.sftp [2.2.0.v20190425-2127,2.2.0.v20190425-2127]
 	org.apache.sshd.sftp.source [2.2.0.v20190425-2127,2.2.0.v20190425-2127]
 }
+

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

 package org.eclipse.jgit.pgm;
 
 import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
 
-import java.util.ArrayList;
 import java.util.Arrays;
-import java.util.List;
+import java.util.HashMap;
+import java.util.Map;
 
 import org.eclipse.jgit.api.Git;
 import org.eclipse.jgit.lib.CLIRepositoryTestCase;
-import org.eclipse.jgit.util.FS;
 import org.eclipse.jgit.util.SystemReader;
 import org.junit.Before;
 import org.junit.Test;
 		}
 	}
 
+	@SuppressWarnings("boxing")
 	@Test
 	public void testListConfig() throws Exception {
 		boolean isWindows = SystemReader.getInstance().getProperty("os.name")
 				.equals("Mac OS X");
 
 		String[] output = execute("git config --list");
-		List<String> expect = new ArrayList<>();
-		expect.add("gc.autoDetach=false");
-		expect.add("core.filemode=" + !isWindows);
-		expect.add("core.logallrefupdates=true");
-		if (isMac)
-			expect.add("core.precomposeunicode=true");
-		expect.add("core.repositoryformatversion=0");
-		if (!FS.DETECTED.supportsSymlinks())
-			expect.add("core.symlinks=false");
-		expect.add(""); // ends with LF (last line empty)
-		assertEquals("expected default configuration",
-				Arrays.asList(expect.toArray()).toString(),
-				Arrays.asList(output).toString());
+
+		Map<String, String> options = parseOptions(output);
+
+		assertEquals(!isWindows, Boolean.valueOf(options.get("core.filemode")));
+		assertTrue((Boolean.valueOf(options.get("core.logallrefupdates"))));
+		if (isMac) {
+			assertTrue(
+					(Boolean.valueOf(options.get("core.precomposeunicode"))));
+		}
+		assertEquals(Integer.valueOf(0),
+				Integer.valueOf(options.get("core.repositoryformatversion")));
+	}
+
+	private Map<String, String> parseOptions(String[] output) {
+		Map<String, String> options = new HashMap<>();
+		Arrays.stream(output).forEachOrdered(s -> {
+			int p = s.indexOf('=');
+			if (p == -1) {
+				return;
+			}
+			String key = s.substring(0, p);
+			String value = s.substring(p + 1);
+			options.put(key, value);
+		});
+		return options;
 	}
 
 }

org.eclipse.jgit.test/BUILD

     deps = [
         "//lib:jsch",
         "//lib:junit",
+        "//lib:slf4j-simple",
         "//lib:mockito",
         "//org.eclipse.jgit:jgit",
         "//org.eclipse.jgit.junit:junit",

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

 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
 Import-Package: com.googlecode.javaewah;version="[1.1.6,2.0.0)",
  com.jcraft.jsch;version="[0.1.54,0.2.0)",
- net.bytebuddy.dynamic.loading;version="[1.7.0,2.0.0)",
+ net.bytebuddy.dynamic.loading;version="[1.9.0,2.0.0)",
  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.junit.rules;version="[4.12,5.0.0)",
  org.junit.runner;version="[4.12,5.0.0)",
  org.junit.runners;version="[4.12,5.0.0)",
- org.mockito;version="[2.13.0,3.0.0)",
- org.mockito.invocation;version="[2.13.0,3.0.0)",
- org.mockito.junit;version="[2.13.0,3.0.0)",
- org.mockito.stubbing;version="[2.13.0,3.0.0)",
+ org.mockito;version="[2.23.0,3.0.0)",
+ org.mockito.invocation;version="[2.23.0,3.0.0)",
+ org.mockito.junit;version="[2.23.0,3.0.0)",
+ org.mockito.stubbing;version="[2.23.0,3.0.0)",
  org.objenesis;version="[2.6.0,3.0.0)",
  org.slf4j;version="[1.7.0,2.0.0)",
  org.tukaani.xz;version="[1.6.0,2.0)"

org.eclipse.jgit.test/pom.xml

     <dependency>
       <groupId>org.mockito</groupId>
       <artifactId>mockito-core</artifactId>
-      <version>2.13.0</version>
+      <version>2.23.0</version>
     </dependency>
 
     <dependency>

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

 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.appender.fileLogger.bufferedIO = true
+log4j.appender.fileLogger.bufferSize = 4096
 
 #log4j.logger.org.eclipse.jgit.util.FS = DEBUG
 #log4j.logger.org.eclipse.jgit.internal.storage.file.FileSnapshot = DEBUG

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

+org.slf4j.simpleLogger.logFile = System.err
+org.slf4j.simpleLogger.cacheOutputStream = true
+org.slf4j.simpleLogger.defaultLogLevel = info
+org.slf4j.simpleLogger.showDateTime = true
+org.slf4j.simpleLogger.dateTimeFormat = HH:mm:ss.SSSXXX
+org.slf4j.simpleLogger.showThreadName = true
+
+#org.slf4j.simpleLogger.log.org.eclipse.jgit.util.FS = debug
+#org.slf4j.simpleLogger.log.org.eclipse.jgit.internal.storage.file.FileSnapshot = debug

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

 import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.lib.Ref;
 import org.eclipse.jgit.lib.Repository;
+import org.eclipse.jgit.lib.StoredConfig;
 import org.eclipse.jgit.revwalk.RevBlob;
 import org.eclipse.jgit.revwalk.RevCommit;
-import org.eclipse.jgit.storage.file.FileBasedConfig;
 import org.eclipse.jgit.submodule.SubmoduleStatus;
 import org.eclipse.jgit.submodule.SubmoduleStatusType;
 import org.eclipse.jgit.submodule.SubmoduleWalk;
 				ConfigConstants.CONFIG_BRANCH_SECTION, "test",
 				ConfigConstants.CONFIG_KEY_REBASE, null));
 
-		FileBasedConfig userConfig = SystemReader.getInstance().openUserConfig(
-				null, git.getRepository().getFS());
+		StoredConfig userConfig = SystemReader.getInstance()
+				.getUserConfig();
 		userConfig.setString(ConfigConstants.CONFIG_BRANCH_SECTION, null,
 				ConfigConstants.CONFIG_KEY_AUTOSETUPREBASE,
 				ConfigConstants.CONFIG_KEY_ALWAYS);

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

 		try {
 			final Repository repo = git.getRepository();
 			final ObjectId headId = repo.resolve(Constants.HEAD + "^{commit}");
+			if (headId == null) {
+				return "";
+			}
 			try (RevWalk rw = new RevWalk(repo)) {
 				final TreeWalk tw = TreeWalk.forPath(repo, path,
 						rw.parseTree(headId));
+				if (tw == null) {
+					return "";
+				}
 				return new String(tw.getObjectReader().open(tw.getObjectId(0))
 						.getBytes(), UTF_8);
 			}

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

 import java.util.ArrayList;
 import java.util.concurrent.TimeUnit;
 
+import org.eclipse.jgit.junit.MockSystemReader;
 import org.eclipse.jgit.util.FS;
 import org.eclipse.jgit.util.FS.FileStoreAttributes;
 import org.eclipse.jgit.util.FileUtils;
 
 	@Before
 	public void setUp() throws Exception {
+		SystemReader.setInstance(new MockSystemReader());
 		trash = Files.createTempDirectory("tmp_");
 		// measure timer resolution before the test to avoid time critical tests
 		// are affected by time needed for measurement

org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/reftree/LocalDiskRefTreeDatabaseTest.java

 	@Override
 	@Before
 	public void setUp() throws Exception {
+		super.setUp();
 		FileRepository init = createWorkRepository();
 		FileBasedConfig cfg = init.getConfig();
 		cfg.setInt("core", null, "repositoryformatversion", 1);

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

 import java.util.StringTokenizer;
 
 import org.eclipse.jgit.errors.ConfigInvalidException;
+import org.eclipse.jgit.junit.MockSystemReader;
 import org.eclipse.jgit.util.FS;
 import org.eclipse.jgit.util.FileUtils;
 import org.eclipse.jgit.util.IO;
+import org.eclipse.jgit.util.SystemReader;
 import org.junit.After;
 import org.junit.Before;
 import org.junit.Test;
 
 	@Before
 	public void setUp() throws Exception {
+		SystemReader.setInstance(new MockSystemReader());
 		trash = Files.createTempDirectory("tmp_");
 		FS.getFileStoreAttributes(trash.getParent());
 	}

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

 import java.util.concurrent.TimeUnit;
 
 import org.eclipse.jgit.errors.CommandFailedException;
+import org.eclipse.jgit.junit.MockSystemReader;
 import org.eclipse.jgit.junit.RepositoryTestCase;
 import org.eclipse.jgit.lib.RepositoryCache;
 import org.junit.After;
 
 	@Before
 	public void setUp() throws Exception {
+		SystemReader.setInstance(new MockSystemReader());
 		trash = File.createTempFile("tmp_", "");
 		trash.delete();
 		assertTrue("mkdir " + trash, trash.mkdir());

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

+/*
+ * Copyright (C) 2019, Vishal Devgire <vishaldevgire@gmail.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.assertFalse;
+import static org.junit.Assert.assertTrue;
+
+import java.io.File;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+
+import org.eclipse.jgit.junit.MockSystemReader;
+import org.eclipse.jgit.lib.ConfigConstants;
+import org.eclipse.jgit.storage.file.FileBasedConfig;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class FS_POSIXTest {
+	private SystemReader originalSystemReaderInstance;
+
+	private FileBasedConfig systemConfig;
+
+	private FileBasedConfig userConfig;
+
+	private Path tmp;
+
+	@Before
+	public void setUp() throws Exception {
+		tmp = Files.createTempDirectory("jgit_test_");
+		MockSystemReader mockSystemReader = new MockSystemReader();
+		SystemReader.setInstance(mockSystemReader);
+
+		// Measure timer resolution before the test to avoid time critical tests
+		// are affected by time needed for measurement.
+		// The MockSystemReader must be configured first since we need to use
+		// the same one here
+		FS.getFileStoreAttributes(tmp.getParent());
+		systemConfig = new FileBasedConfig(
+				new File(tmp.toFile(), "systemgitconfig"), FS.DETECTED);
+		userConfig = new FileBasedConfig(systemConfig,
+				new File(tmp.toFile(), "usergitconfig"), FS.DETECTED);
+		// We have to set autoDetach to false for tests, because tests expect to
+		// be able to clean up by recursively removing the repository, and
+		// background GC might be in the middle of writing or deleting files,
+		// which would disrupt this.
+		userConfig.setBoolean(ConfigConstants.CONFIG_GC_SECTION, null,
+				ConfigConstants.CONFIG_KEY_AUTODETACH, false);
+		userConfig.save();
+		mockSystemReader.setSystemGitConfig(systemConfig);
+		mockSystemReader.setUserGitConfig(userConfig);
+
+		originalSystemReaderInstance = SystemReader.getInstance();
+		SystemReader.setInstance(mockSystemReader);
+	}
+
+	@After
+	public void tearDown() throws IOException {
+		SystemReader.setInstance(originalSystemReaderInstance);
+		FileUtils.delete(tmp.toFile(), FileUtils.RECURSIVE | FileUtils.RETRY);
+	}
+
+	@Test
+	public void supportsAtomicCreateNewFile_shouldReturnSupportedAsDefault() {
+		assertTrue(new FS_POSIX().supportsAtomicCreateNewFile());
+	}
+
+	@Test
+	public void supportsAtomicCreateNewFile_shouldReturnTrueIfFlagIsSetInUserConfig() {
+		setAtomicCreateCreationFlag(userConfig, "true");
+		assertTrue(new FS_POSIX().supportsAtomicCreateNewFile());
+	}
+
+	@Test
+	public void supportsAtomicCreateNewFile_shouldReturnTrueIfFlagIsSetInSystemConfig() {
+		setAtomicCreateCreationFlag(systemConfig, "true");
+		assertTrue(new FS_POSIX().supportsAtomicCreateNewFile());
+	}
+
+	@Test
+	public void supportsAtomicCreateNewFile_shouldReturnFalseIfFlagUnsetInUserConfig() {
+		setAtomicCreateCreationFlag(userConfig, "false");
+		assertFalse(new FS_POSIX().supportsAtomicCreateNewFile());
+	}
+
+	@Test
+	public void supportsAtomicCreateNewFile_shouldReturnFalseIfFlagUnsetInSystemConfig() {
+		setAtomicCreateCreationFlag(systemConfig, "false");
+		assertFalse(new FS_POSIX().supportsAtomicCreateNewFile());
+	}
+
+	private void setAtomicCreateCreationFlag(FileBasedConfig config,
+			String value) {
+		config.setString(ConfigConstants.CONFIG_CORE_SECTION, null,
+				ConfigConstants.CONFIG_KEY_SUPPORTSATOMICFILECREATION, value);
+	}
+}

org.eclipse.jgit/.settings/.api_filters

             </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_arguments>
         </filter>
     </resource>
+    <resource path="src/org/eclipse/jgit/util/SystemReader.java" type="org.eclipse.jgit.util.SystemReader">
+        <filter id="336695337">
+            <message_arguments>
+                <message_argument value="org.eclipse.jgit.util.SystemReader"/>
+                <message_argument value="getSystemConfig()"/>
+            </message_arguments>
+        </filter>
+        <filter id="336695337">
+            <message_arguments>
+                <message_argument value="org.eclipse.jgit.util.SystemReader"/>
+                <message_argument value="getUserConfig()"/>
+            </message_arguments>
+        </filter>
+        <filter id="1142947843">
+            <message_arguments>
+                <message_argument value="5.1.9"/>
+                <message_argument value="getSystemConfig()"/>
+            </message_arguments>
+        </filter>
+        <filter id="1142947843">
+            <message_arguments>
+                <message_argument value="5.1.9"/>
+                <message_argument value="getUserConfig()"/>
+            </message_arguments>
+        </filter>
+    </resource>
 </component>

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

 archiveFormatAlreadyAbsent=Archive format already absent: {0}
 archiveFormatAlreadyRegistered=Archive format already registered with different implementation: {0}
 argumentIsNotAValidCommentString=Invalid comment: {0}
+assumeAtomicCreateNewFile=Reading option "core.supportsAtomicFileCreation" failed, fallback to default assuming atomic file creation is supported
 atLeastOnePathIsRequired=At least one path is required.
 atLeastOnePatternIsRequired=At least one pattern is required.
 atLeastTwoFiltersNeeded=At least two filters needed.
 expectedReceivedContentType=expected Content-Type {0}; received Content-Type {1}
 expectedReportForRefNotReceived={0}: expected report for ref {1} not received
 failedAtomicFileCreation=Atomic file creation failed, number of hard links to file {0} was not 2 but {1}
+failedCreateLockFile=Creating lock file {} failed
 failedToDetermineFilterDefinition=An exception occurred while determining filter definitions
 failedUpdatingRefs=failed updating refs
 failureDueToOneOfTheFollowing=Failure due to one of the following:
 localRepository=local repository
 lockCountMustBeGreaterOrEqual1=lockCount must be >= 1
 lockError=lock error: {0}
+lockFailedRetry=locking {0} failed after {1} retries
 lockOnNotClosed=Lock on {0} not closed.
 lockOnNotHeld=Lock on {0} not held.
 malformedpersonIdentString=Malformed PersonIdent string (no < was found): {0}
 pushOptionsNotSupported=Push options not supported; received {0}
 rawLogMessageDoesNotParseAsLogEntry=Raw log message does not parse as log entry
 readConfigFailed=Reading config file ''{0}'' failed
+readFileStoreAttributesFailed=Reading FileStore attributes from user config failed
 readerIsRequired=Reader is required
 readingObjectsFromLocalRepositoryFailed=reading objects from local repository failed: {0}
 readLastModifiedFailed=Reading lastModified of {0} failed
 s3ActionReading=Reading
 s3ActionWriting=Writing
 searchForReachableBranches=Finding reachable branches
+saveFileStoreAttributesFailed=Saving measured FileStore attributes to user config failed
 searchForReuse=Finding sources
 searchForSizes=Getting sizes
 secondsAgo={0} seconds ago
 uriNotFound={0} not found
 uriNotFoundWithMessage={0} not found: {1}
 URINotSupported=URI not supported: {0}
-userConfigFileInvalid=User config file {0} invalid {1}
+userConfigInvalid=Git config in the user's home directory {0} is invalid {1}
 validatingGitModules=Validating .gitmodules files
 walkFailure=Walk failure.
 wantNoSpaceWithCapabilities=No space between oid and first capability in first want line

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

 	/***/ public String archiveFormatAlreadyAbsent;
 	/***/ public String archiveFormatAlreadyRegistered;
 	/***/ public String argumentIsNotAValidCommentString;
+	/***/ public String assumeAtomicCreateNewFile;
 	/***/ public String atLeastOnePathIsRequired;
 	/***/ public String atLeastOnePatternIsRequired;
 	/***/ public String atLeastTwoFiltersNeeded;
 	/***/ public String expectedReceivedContentType;
 	/***/ public String expectedReportForRefNotReceived;
 	/***/ public String failedAtomicFileCreation;
+	/***/ public String failedCreateLockFile;
 	/***/ public String failedToDetermineFilterDefinition;
 	/***/ public String failedUpdatingRefs;
 	/***/ public String failureDueToOneOfTheFollowing;
 	/***/ public String localRepository;
 	/***/ public String lockCountMustBeGreaterOrEqual1;
 	/***/ public String lockError;
+	/***/ public String lockFailedRetry;
 	/***/ public String lockOnNotClosed;
 	/***/ public String lockOnNotHeld;
 	/***/ public String malformedpersonIdentString;
 	/***/ public String pushOptionsNotSupported;
 	/***/ public String rawLogMessageDoesNotParseAsLogEntry;
 	/***/ public String readConfigFailed;
+	/***/ public String readFileStoreAttributesFailed;
 	/***/ public String readerIsRequired;
 	/***/ public String readingObjectsFromLocalRepositoryFailed;
 	/***/ public String readLastModifiedFailed;
 	/***/ public String s3ActionDeletion;
 	/***/ public String s3ActionReading;
 	/***/ public String s3ActionWriting;
+	/***/ public String saveFileStoreAttributesFailed;
 	/***/ public String searchForReachableBranches;
 	/***/ public String searchForReuse;
 	/***/ public String searchForSizes;
 	/***/ public String uriNotFound;
 	/***/ public String uriNotFoundWithMessage;
 	/***/ public String URINotSupported;
-	/***/ public String userConfigFileInvalid;
+	/***/ public String userConfigInvalid;
 	/***/ public String validatingGitModules;
 	/***/ public String walkFailure;
 	/***/ public String wantNoSpaceWithCapabilities;

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

 import org.eclipse.jgit.lib.RefUpdate;
 import org.eclipse.jgit.lib.ReflogReader;
 import org.eclipse.jgit.lib.Repository;
+import org.eclipse.jgit.lib.StoredConfig;
 import org.eclipse.jgit.storage.file.FileBasedConfig;
 import org.eclipse.jgit.storage.file.FileRepositoryBuilder;
 import org.eclipse.jgit.storage.pack.PackConfig;
-import org.eclipse.jgit.util.FS;
 import org.eclipse.jgit.util.FileUtils;
 import org.eclipse.jgit.util.IO;
 import org.eclipse.jgit.util.RawParseUtils;
 import org.eclipse.jgit.util.StringUtils;
 import org.eclipse.jgit.util.SystemReader;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 /**
  * Represents a Git repository. A repository holds all objects and refs used for
  * This implementation only handles a subtly undocumented subset of git features.
  */
 public class FileRepository extends Repository {
+	private static final Logger LOG = LoggerFactory
+			.getLogger(FileRepository.class);
 	private static final String UNNAMED = "Unnamed repository; edit this file to name it for gitweb."; //$NON-NLS-1$
 
-	private final FileBasedConfig systemConfig;
-	private final FileBasedConfig userConfig;
 	private final FileBasedConfig repoConfig;
 	private final RefDatabase refs;
 	private final ObjectDirectory objectDatabase;
 	 */
 	public FileRepository(BaseRepositoryBuilder options) throws IOException {
 		super(options);
-
-		if (StringUtils.isEmptyOrNull(SystemReader.getInstance().getenv(
-				Constants.GIT_CONFIG_NOSYSTEM_KEY)))
-			systemConfig = SystemReader.getInstance().openSystemConfig(null,
-					getFS());
-		else
-			systemConfig = new FileBasedConfig(null, FS.DETECTED) {
-				@Override
-				public void load() {
-					// empty, do not load
-				}
-
-				@Override
-				public boolean isOutdated() {
-					// regular class would bomb here
-					return false;
-				}
-			};
-		userConfig = SystemReader.getInstance().openUserConfig(systemConfig,
-				getFS());
+		StoredConfig userConfig = null;
+		try {
+			userConfig = SystemReader.getInstance().getUserConfig();
+		} catch (ConfigInvalidException e) {
+			LOG.error(e.getMessage(), e);
+			throw new IOException(e.getMessage(), e);
+		}
 		repoConfig = new FileBasedConfig(userConfig, getFS().resolve(
 				getDirectory(), Constants.CONFIG),
 				getFS());
-
-		loadSystemConfig();
-		loadUserConfig();
 		loadRepoConfig();
 
 		repoConfig.addChangeListener(this::fireEvent);
 		}
 	}
 
-	private void loadSystemConfig() throws IOException {
-		try {
-			systemConfig.load();
-		} catch (ConfigInvalidException e) {
-			throw new IOException(MessageFormat.format(JGitText
-					.get().systemConfigFileInvalid, systemConfig.getFile()
-							.getAbsolutePath(),
-					e), e);
-		}
-	}
-
-	private void loadUserConfig() throws IOException {
-		try {
-			userConfig.load();
-		} catch (ConfigInvalidException e) {
-			throw new IOException(MessageFormat.format(JGitText
-					.get().userConfigFileInvalid, userConfig.getFile()
-							.getAbsolutePath(),
-					e), e);
-		}
-	}
-
 	private void loadRepoConfig() throws IOException {
 		try {
 			repoConfig.load();
 	/** {@inheritDoc} */
 	@Override
 	public FileBasedConfig getConfig() {
-		if (systemConfig.isOutdated()) {
-			try {
-				loadSystemConfig();
-			} catch (IOException e) {
-				throw new RuntimeException(e);
-			}
-		}
-		if (userConfig.isOutdated()) {
-			try {
-				loadUserConfig();
-			} catch (IOException e) {
-				throw new RuntimeException(e);
+		try {
+			SystemReader.getInstance().getUserConfig();
+			if (repoConfig.isOutdated()) {
+				loadRepoConfig();
 			}
-		}
-		if (repoConfig.isOutdated()) {
-				try {
-					loadRepoConfig();
-				} catch (IOException e) {
-					throw new RuntimeException(e);
-				}
+		} catch (IOException | ConfigInvalidException e) {
+			throw new RuntimeException(e);
 		}
 		return repoConfig;
 	}

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

 	 */
 	public boolean lock() throws IOException {
 		FileUtils.mkdirs(lck.getParentFile(), true);
-		token = FS.DETECTED.createNewFileAtomic(lck);
+		try {
+			token = FS.DETECTED.createNewFileAtomic(lck);
+		} catch (IOException e) {
+			LOG.error(JGitText.get().failedCreateLockFile, lck, e);
+			throw e;
+		}
 		if (token.isCreated()) {
 			haveLck = true;
 			try {

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

 	 */
 	@SuppressWarnings("unchecked")
 	public V get(AnyObjectId toFind) {
+		if (toFind == null) {
+			return null;
+		}
 		int h = toFind.w1;
 		V obj = directory[h & mask][h >>> SEGMENT_SHIFT];
 		for (; obj != null; obj = (V) obj.next)

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

 			if (skip != -1) {
 				// try to parse the line as non-comment
 				line = parseLine(buf, skip, lineEnd);
-				// successfully parsed as non-comment line
-				// mark this line as a comment explicitly
-				line.setAction(Action.COMMENT);
-				// use the read line as comment string
-				line.setComment(commentString);
+				if (line != null) {
+					// successfully parsed as non-comment line
+					// mark this line as a comment explicitly
+					line.setAction(Action.COMMENT);
+					// use the read line as comment string
+					line.setComment(commentString);
+				}
 			}
 		} catch (Exception e) {
 			// parsing as non-comment line failed

org.eclipse.jgit/src/org/eclipse/jgit/storage/file/FileBasedConfig.java

 	 */
 	@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;
-			if (useFileSnapshotWithConfig) {
-				newSnapshot = FileSnapshot.save(getFile());
-			} else {
-				// don't use config in this snapshot to avoid endless recursion
-				newSnapshot = FileSnapshot.saveNoConfig(getFile());
-			}
+			// 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);

org.eclipse.jgit/src/org/eclipse/jgit/transport/HttpConfig.java

 import org.eclipse.jgit.errors.ConfigInvalidException;
 import org.eclipse.jgit.internal.JGitText;
 import org.eclipse.jgit.lib.Config;
-import org.eclipse.jgit.storage.file.FileBasedConfig;
-import org.eclipse.jgit.util.FS;
+import org.eclipse.jgit.lib.StoredConfig;
 import org.eclipse.jgit.util.StringUtils;
 import org.eclipse.jgit.util.SystemReader;
 import org.slf4j.Logger;
 	 *            to get the configuration values for
 	 */
 	public HttpConfig(URIish uri) {
-		FileBasedConfig userConfig = SystemReader.getInstance()
-				.openUserConfig(null, FS.DETECTED);
+		StoredConfig userConfig = null;
 		try {
-			userConfig.load();
+			userConfig = SystemReader.getInstance().getUserConfig();
 		} catch (IOException | ConfigInvalidException e) {
 			// Log it and then work with default values.
-			LOG.error(MessageFormat.format(JGitText.get().userConfigFileInvalid,
-					userConfig.getFile().getAbsolutePath(), e));
+			LOG.error(e.getMessage(), e);
 			init(new Config(), uri);
 			return;
 		}

org.eclipse.jgit/src/org/eclipse/jgit/transport/TransportHttp.java

 import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.lib.StoredConfig;
 import org.eclipse.jgit.lib.SymbolicRef;
-import org.eclipse.jgit.storage.file.FileBasedConfig;
 import org.eclipse.jgit.transport.HttpAuthMethod.Type;
 import org.eclipse.jgit.transport.HttpConfig.HttpRedirectMode;
 import org.eclipse.jgit.transport.http.HttpConnection;
-import org.eclipse.jgit.util.FS;
 import org.eclipse.jgit.util.HttpSupport;
 import org.eclipse.jgit.util.IO;
 import org.eclipse.jgit.util.RawParseUtils;
 	}
 
 	private void updateSslVerifyUser(boolean value) {
-		FileBasedConfig userConfig = SystemReader.getInstance()
-				.openUserConfig(null, FS.DETECTED);
+		StoredConfig userConfig = null;
 		try {
-			userConfig.load();
+			userConfig = SystemReader.getInstance().getUserConfig();
 			updateSslVerify(userConfig, value);
 		} catch (IOException | ConfigInvalidException e) {
 			// Log it, but otherwise ignore here.
-			LOG.error(MessageFormat.format(JGitText.get().userConfigFileInvalid,
-					userConfig.getFile().getAbsolutePath(), e));
+			LOG.error(e.getMessage(), e);
 		}
 	}
 

org.eclipse.jgit/src/org/eclipse/jgit/util/FS.java

 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.lib.StoredConfig;
 import org.eclipse.jgit.treewalk.FileTreeIterator.FileEntry;
 import org.eclipse.jgit.treewalk.FileTreeIterator.FileModeStrategy;
 import org.eclipse.jgit.treewalk.WorkingTreeIterator.Entry;
 
 		private static Optional<FileStoreAttributes> readFromConfig(
 				FileStore s) {
-			FileBasedConfig userConfig = SystemReader.getInstance()
-					.openUserConfig(null, FS.DETECTED);
+			StoredConfig userConfig;
 			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()));
+				userConfig = SystemReader.getInstance().getUserConfig();
+			} catch (IOException | ConfigInvalidException e) {
+				LOG.error(JGitText.get().readFileStoreAttributesFailed, e);
+				return Optional.empty();
 			}
 			String key = getConfigKey(s);
 			Duration resolution = Duration.ofNanos(userConfig.getTimeUnit(
 
 		private static void saveToConfig(FileStore s,
 				FileStoreAttributes c) {
-			FileBasedConfig userConfig = SystemReader.getInstance()
-					.openUserConfig(null, FS.DETECTED);
+			StoredConfig userConfig;
+			try {
+				userConfig = SystemReader.getInstance().getUserConfig();
+			} catch (IOException | ConfigInvalidException e) {
+				LOG.error(JGitText.get().saveFileStoreAttributesFailed, e);
+				return;
+			}
 			long resolution = c.getFsTimestampResolution().toNanos();
 			TimeUnit resolutionUnit = getUnit(resolution);
 			long resolutionValue = resolutionUnit.convert(resolution,
 			String key = getConfigKey(s);
 			while (!succeeded && retries < max_retries) {
 				try {
-					userConfig.load(false);
+					userConfig.load();
 					userConfig.setString(
 							ConfigConstants.CONFIG_FILESYSTEM_SECTION, key,
 							ConfigConstants.CONFIG_KEY_TIMESTAMP_RESOLUTION,
 				} 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);
+						if (retries < max_retries) {
+							Thread.sleep(100);
+							LOG.debug("locking {} failed, retries {}/{}", //$NON-NLS-1$
+									userConfig, Integer.valueOf(retries),
+									Integer.valueOf(max_retries));
+						} else {
+							LOG.warn(MessageFormat.format(
+									JGitText.get().lockFailedRetry, userConfig,
+									Integer.valueOf(retries)));
+						}
 					} catch (InterruptedException e1) {
-						Thread.interrupted();
+						Thread.currentThread().interrupt();
+						break;
 					}
 				} catch (IOException e) {
 					LOG.error(MessageFormat.format(
-							JGitText.get().cannotSaveConfig,
-							userConfig.getFile().getAbsolutePath()), e);
+							JGitText.get().cannotSaveConfig, userConfig), e);
+					break;
 				} catch (ConfigInvalidException e) {
 					LOG.error(MessageFormat.format(
 							JGitText.get().repositoryConfigFileInvalid,
-							userConfig.getFile().getAbsolutePath(),
-							e.getMessage()));
+							userConfig, e.getMessage()));
+					break;
 				}
 			}
 		}

org.eclipse.jgit/src/org/eclipse/jgit/util/FS_POSIX.java

  */
 package org.eclipse.jgit.util;
 
+import static org.eclipse.jgit.lib.ConfigConstants.CONFIG_CORE_SECTION;
+import static org.eclipse.jgit.lib.ConfigConstants.CONFIG_KEY_SUPPORTSATOMICFILECREATION;
+
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.IOException;
 import java.io.InputStreamReader;
 import java.io.PrintStream;
 import java.nio.charset.Charset;
+import java.nio.file.FileAlreadyExistsException;
 import java.nio.file.FileStore;
 import java.nio.file.FileSystemException;
 import java.nio.file.Files;
+import java.nio.file.InvalidPathException;
 import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.nio.file.attribute.PosixFilePermission;
 import org.eclipse.jgit.errors.CommandFailedException;
 import org.eclipse.jgit.errors.ConfigInvalidException;
 import org.eclipse.jgit.internal.JGitText;
-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.lib.StoredConfig;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 
 	private static final Map<FileStore, Boolean> CAN_HARD_LINK = new ConcurrentHashMap<>();
 
-	private volatile AtomicFileCreation supportsAtomicCreateNewFile = AtomicFileCreation.UNDEFINED;
+	private volatile AtomicFileCreation supportsAtomicFileCreation = AtomicFileCreation.UNDEFINED;
 
 	private enum AtomicFileCreation {
 		SUPPORTED, NOT_SUPPORTED, UNDEFINED
 		}
 	}
 
-	private void determineAtomicFileCreationSupport() {
-		// @TODO: enhance SystemReader to support this without copying code
-		AtomicFileCreation ret = getAtomicFileCreationSupportOption(
-				SystemReader.getInstance().openUserConfig(null, this));
-		if (ret == AtomicFileCreation.UNDEFINED
-				&& StringUtils.isEmptyOrNull(SystemReader.getInstance()
-						.getenv(Constants.GIT_CONFIG_NOSYSTEM_KEY))) {
-			ret = getAtomicFileCreationSupportOption(
-					SystemReader.getInstance().openSystemConfig(null, this));
-		}
-		supportsAtomicCreateNewFile = ret;
-	}
-
-	private AtomicFileCreation getAtomicFileCreationSupportOption(
-			FileBasedConfig config) {
-		try {
-			config.load();
-			String value = config.getString(ConfigConstants.CONFIG_CORE_SECTION,
-					null,
-					ConfigConstants.CONFIG_KEY_SUPPORTSATOMICFILECREATION);
-			if (value == null) {
-				return AtomicFileCreation.UNDEFINED;
-			}
-			return StringUtils.toBoolean(value)
-					? AtomicFileCreation.SUPPORTED
-					: AtomicFileCreation.NOT_SUPPORTED;
-		} catch (IOException | ConfigInvalidException e) {
-			return AtomicFileCreation.SUPPORTED;
-		}
-	}
-
 	/** {@inheritDoc} */
 	@Override
 	public FS newInstance() {
 	/** {@inheritDoc} */
 	@Override
 	public boolean supportsAtomicCreateNewFile() {
-		if (supportsAtomicCreateNewFile == AtomicFileCreation.UNDEFINED) {
-			determineAtomicFileCreationSupport();
+		if (supportsAtomicFileCreation == AtomicFileCreation.UNDEFINED) {
+			try {
+				StoredConfig config = SystemReader.getInstance().getUserConfig();
+				String value = config.getString(CONFIG_CORE_SECTION, null,
+						CONFIG_KEY_SUPPORTSATOMICFILECREATION);
+				if (value != null) {
+					supportsAtomicFileCreation = StringUtils.toBoolean(value)
+							? AtomicFileCreation.SUPPORTED
+							: AtomicFileCreation.NOT_SUPPORTED;
+				} else {
+					supportsAtomicFileCreation = AtomicFileCreation.SUPPORTED;
+				}
+			} catch (IOException | ConfigInvalidException e) {
+				LOG.warn(JGitText.get().assumeAtomicCreateNewFile, e);
+				supportsAtomicFileCreation = AtomicFileCreation.SUPPORTED;
+			}
 		}
-		return supportsAtomicCreateNewFile == AtomicFileCreation.SUPPORTED;
+		return supportsAtomicFileCreation == AtomicFileCreation.SUPPORTED;
 	}
 
 	@Override
 	 * An implementation of the File#createNewFile() semantics which can create
 	 * a unique file atomically also on NFS. If the config option
 	 * {@code core.supportsAtomicCreateNewFile = true} (which is the default)
-	 * then simply File#createNewFile() is called.
+	 * then simply Files#createFile() is called.
 	 *
 	 * But if {@code core.supportsAtomicCreateNewFile = false} then after
 	 * successful creation of the lock file a hard link to that lock file is
 	 */
 	@Override
 	public LockToken createNewFileAtomic(File file) throws IOException {
-		if (!file.createNewFile()) {
+		Path path;
+		try {
+			path = file.toPath();
+			Files.createFile(path);
+		} catch (FileAlreadyExistsException | InvalidPathException e) {
 			return token(false, null);
 		}
 		if (supportsAtomicCreateNewFile()) {
 			return token(true, null);
 		}
 		Path link = null;
-		Path path = file.toPath();
 		FileStore store = null;
 		try {
 			store = Files.getFileStore(path);

org.eclipse.jgit/src/org/eclipse/jgit/util/FileUtils.java

 import java.nio.file.Files;
 import java.nio.file.InvalidPathException;
 import java.nio.file.LinkOption;
+import java.nio.file.NoSuchFileException;
 import java.nio.file.Path;
 import java.nio.file.StandardCopyOption;
 import java.nio.file.StandardOpenOption;
 		try {
 			return Files.getLastModifiedTime(path, LinkOption.NOFOLLOW_LINKS)
 					.toInstant();
+		} catch (NoSuchFileException e) {
+			LOG.debug(
+					"Cannot read lastModifiedInstant since path {} does not exist", //$NON-NLS-1$
+					path);
+			return Instant.EPOCH;
 		} catch (IOException e) {
 			LOG.error(MessageFormat
-					.format(JGitText.get().readLastModifiedFailed, path));
+					.format(JGitText.get().readLastModifiedFailed, path), e);
 			return Instant.ofEpochMilli(path.toFile().lastModified());
 		}
 	}

org.eclipse.jgit/src/org/eclipse/jgit/util/SystemReader.java

 package org.eclipse.jgit.util;
 
 import java.io.File;
+import java.io.IOException;
 import java.net.InetAddress;
 import java.net.UnknownHostException;
 import java.security.AccessController;
 import java.util.Locale;
 import java.util.TimeZone;
 
+import org.eclipse.jgit.errors.ConfigInvalidException;
 import org.eclipse.jgit.errors.CorruptObjectException;
 import org.eclipse.jgit.lib.Config;
+import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.ObjectChecker;
+import org.eclipse.jgit.lib.StoredConfig;
 import org.eclipse.jgit.storage.file.FileBasedConfig;
 import org.eclipse.jgit.util.time.MonotonicClock;
 import org.eclipse.jgit.util.time.MonotonicSystemClock;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 /**
  * Interface to read values from the system.
  * </p>
  */
 public abstract class SystemReader {
+
+	private final static Logger LOG = LoggerFactory
+			.getLogger(SystemReader.class);
+
 	private static final SystemReader DEFAULT;
 
 	private static Boolean isMacOS;
 	private static class Default extends SystemReader {
 		private volatile String hostname;
 
+		private volatile FileBasedConfig systemConfig;
+
+		private volatile FileBasedConfig userConfig;
+
 		@Override
 		public String getenv(String variable) {
 			return System.getenv(variable);
 
 		@Override
 		public FileBasedConfig openSystemConfig(Config parent, FS fs) {
-			File configFile = fs.getGitSystemConfig();
-			if (configFile == null) {
-				return new FileBasedConfig(parent, null, fs) {
-					@Override
-					public void load() {
-						// empty, do not load
-					}
-
-					@Override
-					public boolean isOutdated() {
-						// regular class would bomb here
-						return false;
-					}
-				};
+			if (systemConfig == null) {
+				systemConfig = createSystemConfig(parent, fs);
 			}
-			return new FileBasedConfig(parent, configFile, fs);
+			return systemConfig;
+		}
+
+		protected FileBasedConfig createSystemConfig(Config parent, FS fs) {
+			if (StringUtils.isEmptyOrNull(getenv(Constants.GIT_CONFIG_NOSYSTEM_KEY))) {
+				File configFile = fs.getGitSystemConfig();
+				if (configFile != null) {
+					return new FileBasedConfig(parent, configFile, fs);
+				}
+			}
+			return new FileBasedConfig(null, fs) {
+				@Override
+				public void load() {
+					// empty, do not load
+				}
+
+				@Override
+				public boolean isOutdated() {
+					// regular class would bomb here
+					return false;
+				}
+			};
 		}
 
 		@Override
 		public FileBasedConfig openUserConfig(Config parent, FS fs) {
-			final File home = fs.userHome();
-			return new FileBasedConfig(parent, new File(home, ".gitconfig"), fs); //$NON-NLS-1$
+			if (userConfig == null) {
+				File home = fs.userHome();
+				userConfig = new FileBasedConfig(parent,
+						new File(home, ".gitconfig"), fs); //$NON-NLS-1$
+			}
+			return userConfig;
+		}
+
+		@Override
+		public StoredConfig getSystemConfig()
+				throws IOException, ConfigInvalidException {
+			if (systemConfig == null) {
+				systemConfig = createSystemConfig(null, FS.DETECTED);
+			}
+			if (systemConfig.isOutdated()) {
+				LOG.debug("loading system config {}", systemConfig); //$NON-NLS-1$
+				systemConfig.load();
+			}
+			return systemConfig;
+		}
+
+		@Override
+		public StoredConfig getUserConfig()
+				throws IOException, ConfigInvalidException {
+			if (userConfig == null) {
+				userConfig = openUserConfig(getSystemConfig(), FS.DETECTED);
+			} else {
+				getSystemConfig();
+			}
+			if (userConfig.isOutdated()) {
+				LOG.debug("loading user config {}", userConfig); //$NON-NLS-1$
+				userConfig.load();
+			}
+			return userConfig;
 		}
 
 		@Override
 		}
 	}
 
-	private static SystemReader INSTANCE = DEFAULT;
+	private static volatile SystemReader INSTANCE = DEFAULT;
 
 	/**
-	 * Get time since epoch, with up to millisecond resolution.
+	 * Get the current SystemReader instance
 	 *
-	 * @return time since epoch, with up to millisecond resolution.
+	 * @return the current SystemReader instance.
 	 */
 	public static SystemReader getInstance() {
 		return INSTANCE;
 	}
 
 	/**
-	 * Set the new instance to use when accessing properties.
+	 * Set a new SystemReader instance to use when accessing properties.
 	 *
 	 * @param newReader
 	 *            the new instance to use when accessing properties, or null for
 	public abstract String getProperty(String key);
 
 	/**
-	 * Open the git configuration found in the user home
+	 * Open the git configuration found in the user home. Use
+	 * {@link #getUserConfig()} to get the current git configuration in the user
+	 * home since it manages automatic reloading when the gitconfig file was
+	 * modified and avoids unnecessary reloads.
 	 *
 	 * @param parent
 	 *            a config with values not found directly in the returned config
 	public abstract FileBasedConfig openUserConfig(Config parent, FS fs);
 
 	/**
-	 * Open the gitconfig configuration found in the system-wide "etc" directory
+	 * Open the gitconfig configuration found in the system-wide "etc"
+	 * directory. Use {@link #getSystemConfig()} to get the current system-wide
+	 * git configuration since it manages automatic reloading when the gitconfig
+	 * file was modified and avoids unnecessary reloads.
 	 *
 	 * @param parent
 	 *            a config with values not found directly in the returned
 	 */
 	public abstract FileBasedConfig openSystemConfig(Config parent, FS fs);
 
+	/**
+	 * Get the git configuration found in the user home. The configuration will
+	 * be reloaded automatically if the configuration file was modified. Also
+	 * reloads the system config if the system config file was modified. If the
+	 * configuration file wasn't modified returns the cached configuration.
+	 *
+	 * @return the git configuration found in the user home
+	 * @throws ConfigInvalidException
+	 *             if configuration is invalid
+	 * @throws IOException
+	 *             if something went wrong when reading files
+	 * @since 5.1.9
+	 */
+	public abstract StoredConfig getUserConfig()
+			throws IOException, ConfigInvalidException;
+
+	/**
+	 * Get the gitconfig configuration found in the system-wide "etc" directory.
+	 * The configuration will be reloaded automatically if the configuration
+	 * file was modified otherwise returns the cached system level config.
+	 *
+	 * @return the gitconfig configuration found in the system-wide "etc"
+	 *         directory
+	 * @throws ConfigInvalidException
+	 *             if configuration is invalid
+	 * @throws IOException
+	 *             if something went wrong when reading files
+	 * @since 5.1.9
+	 */
+	public abstract StoredConfig getSystemConfig()
+			throws IOException, ConfigInvalidException;
+
 	/**
 	 * Get the current system time
 	 *