Merge branch 'stable-5.2' into stable-5.3

* stable-5.2:
  Prepare 5.1.7-SNAPSHOT builds
  JGit v5.1.6.201903130242-r
  Prepare 4.11.8-SNAPSHOT builds
  JGit v4.11.7.201903122105-r
  Prepare 4.9.10-SNAPSHOT builds
  JGit v4.9.9.201903122025-r
  Prepare 4.7.9-SNAPSHOT builds
  JGit v4.7.8.201903121755-r
  Prepare 4.5.7-SNAPSHOT builds
  JGit v4.5.6.201903121547-r
  Check for packfile validity and fd before reading
  Move throw of PackInvalidException outside the catch
  Use FileSnapshot to get lastModified on PackFile
  Include size when comparing FileSnapshot
  Do not reuse packfiles when changed on filesystem
  Silence API warnings for new API introduced for fixes

Change-Id: Ia866587a910e620cb297bcb2a81fe0786f4e3db2
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>

org.eclipse.jgit/.settings/.api_filters

@@ -1,84 +1,18 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <component id="org.eclipse.jgit" version="2">
-    <resource path="src/org/eclipse/jgit/lib/ObjectIdRef.java" type="org.eclipse.jgit.lib.ObjectIdRef">
-        <filter comment="removing protected constructor breaks implementers which is ok in a minor release following OSGi semantic versioning" id="338722907">
+    <resource path="META-INF/MANIFEST.MF">
+        <filter id="924844039">
             <message_arguments>
-                <message_argument value="org.eclipse.jgit.lib.ObjectIdRef"/>
-                <message_argument value="ObjectIdRef(Ref.Storage, String, ObjectId)"/>
+                <message_argument value="5.3.0"/>
+                <message_argument value="5.3.0"/>
             </message_arguments>
         </filter>
     </resource>
-    <resource path="src/org/eclipse/jgit/lib/Ref.java" type="org.eclipse.jgit.lib.Ref">
-        <filter id="404000815">
+    <resource path="src/org/eclipse/jgit/util/FS.java" type="org.eclipse.jgit.util.FS">
+        <filter id="1142947843">
             <message_arguments>
-                <message_argument value="org.eclipse.jgit.lib.Ref"/>
-                <message_argument value="getUpdateIndex()"/>
-            </message_arguments>
-        </filter>
-    </resource>
-    <resource path="src/org/eclipse/jgit/lib/RefDatabase.java" type="org.eclipse.jgit.lib.RefDatabase">
-        <filter comment="class is extended by extenders but not clients of the API" id="421650549">
-            <message_arguments>
-                <message_argument value="org.eclipse.jgit.lib.RefDatabase"/>
-                <message_argument value="exactRef(String)"/>
-            </message_arguments>
-        </filter>
-        <filter id="421654647">
-            <message_arguments>
-                <message_argument value="org.eclipse.jgit.lib.RefDatabase"/>
-                <message_argument value="getRef(String)"/>
-            </message_arguments>
-        </filter>
-    </resource>
-    <resource path="src/org/eclipse/jgit/transport/BaseReceivePack.java" type="org.eclipse.jgit.transport.BaseReceivePack">
-        <filter id="421650549">
-            <message_arguments>
-                <message_argument value="org.eclipse.jgit.transport.BaseReceivePack"/>
-                <message_argument value="getAdvertisedRefs()"/>
-            </message_arguments>
-        </filter>
-        <filter id="421650549">
-            <message_arguments>
-                <message_argument value="org.eclipse.jgit.transport.BaseReceivePack"/>
-                <message_argument value="getPushCertificate()"/>
-            </message_arguments>
-        </filter>
-        <filter id="421650549">
-            <message_arguments>
-                <message_argument value="org.eclipse.jgit.transport.BaseReceivePack"/>
-                <message_argument value="getRepository()"/>
-            </message_arguments>
-        </filter>
-        <filter id="421650549">
-            <message_arguments>
-                <message_argument value="org.eclipse.jgit.transport.BaseReceivePack"/>
-                <message_argument value="getRevWalk()"/>
-            </message_arguments>
-        </filter>
-        <filter id="421650549">
-            <message_arguments>
-                <message_argument value="org.eclipse.jgit.transport.BaseReceivePack"/>
-                <message_argument value="setAdvertisedRefs(Map&lt;String,Ref&gt;, Set&lt;ObjectId&gt;)"/>
-            </message_arguments>
-        </filter>
-        <filter id="421650549">
-            <message_arguments>
-                <message_argument value="org.eclipse.jgit.transport.BaseReceivePack"/>
-                <message_argument value="setPushCertificate(PushCertificate)"/>
-            </message_arguments>
-        </filter>
-    </resource>
-    <resource path="src/org/eclipse/jgit/transport/TransferConfig.java" type="org.eclipse.jgit.transport.TransferConfig">
-        <filter id="1159725059">
-            <message_arguments>
-                <message_argument value="5.1.4"/>
-                <message_argument value="TransferConfig(Config)"/>
-            </message_arguments>
-        </filter>
-        <filter id="1159725059">
-            <message_arguments>
-                <message_argument value="5.1.4"/>
-                <message_argument value="TransferConfig(Repository)"/>
+                <message_argument value="4.5.6"/>
+                <message_argument value="fileAttributes(File)"/>
             </message_arguments>
         </filter>
     </resource>

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

@@ -45,6 +45,7 @@ package org.eclipse.jgit.internal.storage.file;
 
 import java.io.File;
 import java.io.IOException;
+import java.nio.file.attribute.BasicFileAttributes;
 import java.text.DateFormat;
 import java.text.SimpleDateFormat;
 import java.util.Date;
@@ -69,6 +70,13 @@ import org.eclipse.jgit.util.FS;
  * file is less than 3 seconds ago.
  */
 public class FileSnapshot {
+	/**
+	 * An unknown file size.
+	 *
+	 * This value is used when a comparison needs to happen purely on the lastUpdate.
+	 */
+	public static final long UNKNOWN_SIZE = -1;
+
 	/**
 	 * A FileSnapshot that is considered to always be modified.
 	 * <p>
@@ -76,7 +84,7 @@ public class FileSnapshot {
 	 * file, but only after {@link #isModified(File)} gets invoked. The returned
 	 * snapshot contains only invalid status information.
 	 */
-	public static final FileSnapshot DIRTY = new FileSnapshot(-1, -1);
+	public static final FileSnapshot DIRTY = new FileSnapshot(-1, -1, UNKNOWN_SIZE);
 
 	/**
 	 * A FileSnapshot that is clean if the file does not exist.
@@ -85,7 +93,7 @@ public class FileSnapshot {
 	 * file to be clean. {@link #isModified(File)} will return false if the file
 	 * path does not exist.
 	 */
-	public static final FileSnapshot MISSING_FILE = new FileSnapshot(0, 0) {
+	public static final FileSnapshot MISSING_FILE = new FileSnapshot(0, 0, 0) {
 		@Override
 		public boolean isModified(File path) {
 			return FS.DETECTED.exists(path);
@@ -105,12 +113,16 @@ public class FileSnapshot {
 	public static FileSnapshot save(File path) {
 		long read = System.currentTimeMillis();
 		long modified;
+		long size;
 		try {
-			modified = FS.DETECTED.lastModified(path);
+			BasicFileAttributes fileAttributes = FS.DETECTED.fileAttributes(path);
+			modified = fileAttributes.lastModifiedTime().toMillis();
+			size = fileAttributes.size();
 		} catch (IOException e) {
 			modified = path.lastModified();
+			size = path.length();
 		}
-		return new FileSnapshot(read, modified);
+		return new FileSnapshot(read, modified, size);
 	}
 
 	/**
@@ -125,7 +137,7 @@ public class FileSnapshot {
 	 */
 	public static FileSnapshot save(long modified) {
 		final long read = System.currentTimeMillis();
-		return new FileSnapshot(read, modified);
+		return new FileSnapshot(read, modified, -1);
 	}
 
 	/** Last observed modification time of the path. */
@@ -137,10 +149,16 @@ public class FileSnapshot {
 	/** True once {@link #lastRead} is far later than {@link #lastModified}. */
 	private boolean cannotBeRacilyClean;
 
-	private FileSnapshot(long read, long modified) {
+	/** Underlying file-system size in bytes.
+	 *
+	 * When set to {@link #UNKNOWN_SIZE} the size is not considered for modification checks. */
+	private final long size;
+
+	private FileSnapshot(long read, long modified, long size) {
 		this.lastRead = read;
 		this.lastModified = modified;
 		this.cannotBeRacilyClean = notRacyClean(read);
+		this.size = size;
 	}
 
 	/**
@@ -152,6 +170,13 @@ public class FileSnapshot {
 		return lastModified;
 	}
 
+	/**
+	 * @return file size in bytes of last snapshot update
+	 */
+	public long size() {
+		return size;
+	}
+
 	/**
 	 * Check if the path may have been modified since the snapshot was saved.
 	 *
@@ -161,12 +186,16 @@ public class FileSnapshot {
 	 */
 	public boolean isModified(File path) {
 		long currLastModified;
+		long currSize;
 		try {
-			currLastModified = FS.DETECTED.lastModified(path);
+			BasicFileAttributes fileAttributes = FS.DETECTED.fileAttributes(path);
+			currLastModified = fileAttributes.lastModifiedTime().toMillis();
+			currSize = fileAttributes.size();
 		} catch (IOException e) {
 			currLastModified = path.lastModified();
+			currSize = path.length();
 		}
-		return isModified(currLastModified);
+		return (currSize != UNKNOWN_SIZE && currSize != size) || isModified(currLastModified);
 	}
 
 	/**

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

@@ -914,13 +914,13 @@ public class ObjectDirectory extends FileObjectDatabase {
 			}
 
 			final String packName = base + PACK.getExtension();
+			final File packFile = new File(packDirectory, packName);
 			final PackFile oldPack = forReuse.remove(packName);
-			if (oldPack != null) {
+			if (oldPack != null && oldPack.getFileSnapshot().isModified(packFile)) {
 				list.add(oldPack);
 				continue;
 			}
 
-			final File packFile = new File(packDirectory, packName);
 			list.add(new PackFile(packFile, extensions));
 			foundNew = true;
 		}

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

@@ -131,6 +131,8 @@ public class PackFile implements Iterable<PackIndex.MutableEntry> {
 
 	int packLastModified;
 
+	private FileSnapshot fileSnapshot;
+
 	private volatile boolean invalid;
 
 	private boolean invalidBitmap;
@@ -164,7 +166,8 @@ public class PackFile implements Iterable<PackIndex.MutableEntry> {
 	 */
 	public PackFile(File packFile, int extensions) {
 		this.packFile = packFile;
-		this.packLastModified = (int) (packFile.lastModified() >> 10);
+		this.fileSnapshot = FileSnapshot.save(packFile);
+		this.packLastModified = (int) (fileSnapshot.lastModified() >> 10);
 		this.extensions = extensions;
 
 		// Multiply by 31 here so we can more directly combine with another
@@ -359,6 +362,16 @@ public class PackFile implements Iterable<PackIndex.MutableEntry> {
 		return getReverseIdx().findObject(offset);
 	}
 
+	/**
+	 * Return the @{@link FileSnapshot} associated to the underlying packfile
+	 * that has been used when the object was created.
+	 *
+	 * @return the packfile @{@link FileSnapshot} that the object is loaded from.
+	 */
+	FileSnapshot getFileSnapshot() {
+		return fileSnapshot;
+	}
+
 	private final byte[] decompress(final long position, final int sz,
 			final WindowCursor curs) throws IOException, DataFormatException {
 		byte[] dstbuf;
@@ -647,9 +660,10 @@ public class PackFile implements Iterable<PackIndex.MutableEntry> {
 	}
 
 	private void doOpen() throws IOException {
-		try {
-			if (invalid)
+		if (invalid) {
 			throw new PackInvalidException(packFile);
+		}
+		try {
 			synchronized (readLock) {
 				fd = new RandomAccessFile(packFile, "r"); //$NON-NLS-1$
 				length = fd.length();
@@ -705,6 +719,14 @@ public class PackFile implements Iterable<PackIndex.MutableEntry> {
 
 	ByteArrayWindow read(long pos, int size) throws IOException {
 		synchronized (readLock) {
+			if (invalid || fd == null) {
+				// Due to concurrency between a read and another packfile invalidation thread
+				// one thread could come up to this point and then fail with NPE.
+				// Detect the situation and throw a proper exception so that can be properly
+				// managed by the main packfile search loop and the Git client won't receive
+				// any failures.
+				throw new PackInvalidException(packFile);
+			}
 			if (length < pos + size)
 				size = (int) (length - pos);
 			final byte[] buf = new byte[size];

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

@@ -57,6 +57,7 @@ import java.io.PrintStream;
 import java.nio.charset.Charset;
 import java.nio.file.Files;
 import java.nio.file.Path;
+import java.nio.file.attribute.BasicFileAttributes;
 import java.security.AccessController;
 import java.security.PrivilegedAction;
 import java.text.MessageFormat;
@@ -443,6 +444,19 @@ public abstract class FS {
 	 */
 	public abstract boolean retryFailedLockFileCommit();
 
+	/**
+	 * Return all the attributes of a file, without following symbolic links.
+	 *
+	 * @param file
+	 * @return {@link BasicFileAttributes} of the file
+	 * @throws IOException in case of any I/O errors accessing the file
+	 *
+	 * @since 4.5.6
+	 */
+	public BasicFileAttributes fileAttributes(File file) throws IOException {
+		return FileUtils.fileAttributes(file);
+	}
+
 	/**
 	 * Determine the user's home directory (location where preferences are).
 	 *

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

@@ -659,6 +659,19 @@ public class FileUtils {
 				.toMillis();
 	}
 
+	/**
+	 * Return all the attributes of a file, without following symbolic links.
+	 *
+	 * @param file
+	 * @return {@link BasicFileAttributes} of the file
+	 * @throws IOException in case of any I/O errors accessing the file
+	 *
+	 * @since 4.5.6
+	 */
+	static BasicFileAttributes fileAttributes(File file) throws IOException {
+		return Files.readAttributes(file.toPath(), BasicFileAttributes.class, LinkOption.NOFOLLOW_LINKS);
+	}
+
 	/**
 	 * @param file
 	 * @param time