Merge branch 'stable-5.2' into stable-5.3

* stable-5.2:
  Prepare 5.2.3-SNAPSHOT builds
  JGit v5.2.2.201904231744-r
  Revert 4678f4b and provide another solution for bug 467631
  Apache MINA sshd: make sendKexInit() work also for re-keying
  Prepare 5.1.8-SNAPSHOT builds
  JGit v5.1.7.201904200442-r
  ObjectUploadListener: Add callback interface
  Prepare 4.11.9-SNAPSHOT builds
  JGit v4.11.8.201904181247-r
  Prepare 4.9.11-SNAPSHOT builds
  JGit v4.9.10.201904181027-r
  Prepare 4.7.10-SNAPSHOT builds
  JGit v4.7.9.201904161809-r
  Prepare 4.5.8-SNAPSHOT builds
  JGit v4.5.7.201904151645-r
  Remember the cause for invalidating a packfile
  Fix API problem filters
  Fix pack files scan when filesnapshot isn't modified

Change-Id: Ie7e572ac7e346f21fe0c387d7448be168a9c127a
Signed-off-by: Matthias Sohn <matthias.sohn@sap.com>

8 files changed, 115 insertions, 46 deletions

diff --git a/org.eclipse.jgit/.settings/.api_filters b/org.eclipse.jgit/.settings/.api_filters
index e90d41bfa8..771bdbb2f0 100644
--- a/org.eclipse.jgit/.settings/.api_filters
+++ b/org.eclipse.jgit/.settings/.api_filters
@@ -3,16 +3,22 @@
     <resource path="META-INF/MANIFEST.MF">
         <filter id="924844039">
             <message_arguments>
-                <message_argument value="5.3.0"/>
+                <message_argument value="5.3.1"/>
                 <message_argument value="5.3.0"/>
             </message_arguments>
         </filter>
     </resource>
-    <resource path="src/org/eclipse/jgit/util/FS.java" type="org.eclipse.jgit.util.FS">
+    <resource path="src/org/eclipse/jgit/errors/PackInvalidException.java" type="org.eclipse.jgit.errors.PackInvalidException">
+        <filter id="1142947843">
+            <message_arguments>
+                <message_argument value="4.5.7"/>
+                <message_argument value="PackInvalidException(File, Throwable)"/>
+            </message_arguments>
+        </filter>
         <filter id="1142947843">
             <message_arguments>
-                <message_argument value="4.5.6"/>
-                <message_argument value="fileAttributes(File)"/>
+                <message_argument value="4.5.7"/>
+                <message_argument value="PackInvalidException(String, Throwable)"/>
             </message_arguments>
         </filter>
     </resource>
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/errors/PackInvalidException.java b/org.eclipse.jgit/src/org/eclipse/jgit/errors/PackInvalidException.java
index a83de06262..b238ab4718 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/errors/PackInvalidException.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/errors/PackInvalidException.java
@@ -60,9 +60,24 @@ public class PackInvalidException extends IOException {
 	 *
 	 * @param path
 	 *            path of the invalid pack file.
+	 * @deprecated Use {@link #PackInvalidException(File, Throwable)}.
 	 */
+	@Deprecated
 	public PackInvalidException(File path) {
-		this(path.getAbsolutePath());
+		this(path, null);
+	}
+
+	/**
+	 * Construct a pack invalid error with cause.
+	 *
+	 * @param path
+	 *            path of the invalid pack file.
+	 * @param cause
+	 *            cause of the pack file becoming invalid.
+	 * @since 4.5.7
+	 */
+	public PackInvalidException(File path, Throwable cause) {
+		this(path.getAbsolutePath(), cause);
 	}
 
 	/**
@@ -70,8 +85,23 @@ public class PackInvalidException extends IOException {
 	 *
 	 * @param path
 	 *            path of the invalid pack file.
+	 * @deprecated Use {@link #PackInvalidException(String, Throwable)}.
 	 */
+	@Deprecated
 	public PackInvalidException(String path) {
-		super(MessageFormat.format(JGitText.get().packFileInvalid, path));
+		this(path, null);
+	}
+
+	/**
+	 * Construct a pack invalid error with cause.
+	 *
+	 * @param path
+	 *            path of the invalid pack file.
+	 * @param cause
+	 *            cause of the pack file becoming invalid.
+	 * @since 4.5.7
+	 */
+	public PackInvalidException(String path, Throwable cause) {
+		super(MessageFormat.format(JGitText.get().packFileInvalid, path), cause);
 	}
 }
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/BlockBasedFile.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/BlockBasedFile.java
index 4e4a26f4e6..c7d6c584e4 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/BlockBasedFile.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/BlockBasedFile.java
@@ -83,6 +83,9 @@ abstract class BlockBasedFile {
 	/** True once corruption has been detected that cannot be worked around. */
 	volatile boolean invalid;
 
+	/** Exception that caused the packfile to be flagged as invalid */
+	protected volatile Exception invalidatingCause;
+
 	BlockBasedFile(DfsBlockCache cache, DfsPackDescription desc, PackExt ext) {
 		this.cache = cache;
 		this.key = desc.getStreamKey(ext);
@@ -136,8 +139,9 @@ abstract class BlockBasedFile {
 
 	DfsBlock readOneBlock(long pos, DfsReader ctx, ReadableChannel rc)
 			throws IOException {
-		if (invalid)
-			throw new PackInvalidException(getFileName());
+		if (invalid) {
+			throw new PackInvalidException(getFileName(), invalidatingCause);
+		}
 
 		ctx.stats.readBlock++;
 		long start = System.nanoTime();
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsPackFile.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsPackFile.java
index 451986e831..be1387ed0c 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsPackFile.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsPackFile.java
@@ -181,7 +181,7 @@ public final class DfsPackFile extends BlockBasedFile {
 		}
 
 		if (invalid) {
-			throw new PackInvalidException(getFileName());
+			throw new PackInvalidException(getFileName(), invalidatingCause);
 		}
 
 		Repository.getGlobalListenerList()
@@ -240,6 +240,7 @@ public final class DfsPackFile extends BlockBasedFile {
 				return index;
 			} catch (IOException e) {
 				invalid = true;
+				invalidatingCause = e;
 				throw e;
 			}
 		}
@@ -703,8 +704,10 @@ public final class DfsPackFile extends BlockBasedFile {
 
 	private IOException packfileIsTruncated() {
 		invalid = true;
-		return new IOException(MessageFormat.format(
+		IOException exc = new IOException(MessageFormat.format(
 				JGitText.get().packfileIsTruncated, getFileName()));
+		invalidatingCause = exc;
+		return exc;
 	}
 
 	private void readFully(long position, byte[] dstbuf, int dstoff, int cnt,
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/ObjectDirectory.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/ObjectDirectory.java
index 3ffb8c424d..d502fea020 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/ObjectDirectory.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/ObjectDirectory.java
@@ -132,8 +132,6 @@ public class ObjectDirectory extends FileObjectDatabase {
 
 	private final File alternatesFile;
 
-	private final AtomicReference<PackList> packList;
-
 	private final FS fs;
 
 	private final AtomicReference<AlternateHandle[]> alternates;
@@ -146,6 +144,8 @@ public class ObjectDirectory extends FileObjectDatabase {
 
 	private Set<ObjectId> shallowCommitsIds;
 
+	final AtomicReference<PackList> packList;
+
 	/**
 	 * Initialize a reference to an on-disk object directory.
 	 *
@@ -673,13 +673,8 @@ public class ObjectDirectory extends FileObjectDatabase {
 			transientErrorCount = p.incrementTransientErrorCount();
 		}
 		if (warnTmpl != null) {
-			if (LOG.isDebugEnabled()) {
-				LOG.debug(MessageFormat.format(warnTmpl,
-						p.getPackFile().getAbsolutePath()), e);
-			} else {
-				LOG.warn(MessageFormat.format(warnTmpl,
-						p.getPackFile().getAbsolutePath()));
-			}
+			LOG.warn(MessageFormat.format(warnTmpl,
+					p.getPackFile().getAbsolutePath()), e);
 		} else {
 			if (doLogExponentialBackoff(transientErrorCount)) {
 				// Don't remove the pack from the list, as the error may be
@@ -766,7 +761,7 @@ public class ObjectDirectory extends FileObjectDatabase {
 		return InsertLooseObjectResult.FAILURE;
 	}
 
-	private boolean searchPacksAgain(PackList old) {
+	boolean searchPacksAgain(PackList old) {
 		// Whether to trust the pack folder's modification time. If set
 		// to false we will always scan the .git/objects/pack folder to
 		// check for new pack files. If set to true (default) we use the
@@ -916,7 +911,8 @@ 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 && oldPack.getFileSnapshot().isModified(packFile)) {
+			if (oldPack != null
+					&& !oldPack.getFileSnapshot().isModified(packFile)) {
 				list.add(oldPack);
 				continue;
 			}
@@ -1073,7 +1069,7 @@ public class ObjectDirectory extends FileObjectDatabase {
 		return new File(new File(getDirectory(), d), f);
 	}
 
-	private static final class PackList {
+	static final class PackList {
 		/** State just before reading the pack directory. */
 		final FileSnapshot snapshot;
 
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 ee3c0a8dd9..d834b1a729 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
@@ -135,6 +135,8 @@ public class PackFile implements Iterable<PackIndex.MutableEntry> {
 
 	private volatile boolean invalid;
 
+	private volatile Exception invalidatingCause;
+
 	private boolean invalidBitmap;
 
 	private AtomicInteger transientErrorCount = new AtomicInteger();
@@ -184,7 +186,7 @@ public class PackFile implements Iterable<PackIndex.MutableEntry> {
 				idx = loadedIdx;
 				if (idx == null) {
 					if (invalid) {
-						throw new PackInvalidException(packFile);
+						throw new PackInvalidException(packFile, invalidatingCause);
 					}
 					try {
 						idx = PackIndex.open(extFile(INDEX));
@@ -208,6 +210,7 @@ public class PackFile implements Iterable<PackIndex.MutableEntry> {
 						throw e;
 					} catch (IOException e) {
 						invalid = true;
+						invalidatingCause = e;
 						throw e;
 					}
 				}
@@ -661,7 +664,7 @@ public class PackFile implements Iterable<PackIndex.MutableEntry> {
 
 	private void doOpen() throws IOException {
 		if (invalid) {
-			throw new PackInvalidException(packFile);
+			throw new PackInvalidException(packFile, invalidatingCause);
 		}
 		try {
 			synchronized (readLock) {
@@ -671,13 +674,13 @@ public class PackFile implements Iterable<PackIndex.MutableEntry> {
 			}
 		} catch (InterruptedIOException e) {
 			// don't invalidate the pack, we are interrupted from another thread
-			openFail(false);
+			openFail(false, e);
 			throw e;
 		} catch (FileNotFoundException fn) {
 			// don't invalidate the pack if opening an existing file failed
 			// since it may be related to a temporary lack of resources (e.g.
 			// max open files)
-			openFail(!packFile.exists());
+			openFail(!packFile.exists(), fn);
 			throw fn;
 		} catch (EOFException | AccessDeniedException | NoSuchFileException
 				| CorruptObjectException | NoPackSignatureException
@@ -685,20 +688,21 @@ public class PackFile implements Iterable<PackIndex.MutableEntry> {
 				| UnsupportedPackIndexVersionException
 				| UnsupportedPackVersionException pe) {
 			// exceptions signaling permanent problems with a pack
-			openFail(true);
+			openFail(true, pe);
 			throw pe;
 		} catch (IOException | RuntimeException ge) {
 			// generic exceptions could be transient so we should not mark the
 			// pack invalid to avoid false MissingObjectExceptions
-			openFail(false);
+			openFail(false, ge);
 			throw ge;
 		}
 	}
 
-	private void openFail(boolean invalidate) {
+	private void openFail(boolean invalidate, Exception cause) {
 		activeWindows = 0;
 		activeCopyRawData = 0;
 		invalid = invalidate;
+		invalidatingCause = cause;
 		doClose();
 	}
 
@@ -725,7 +729,7 @@ public class PackFile implements Iterable<PackIndex.MutableEntry> {
 				// 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);
+				throw new PackInvalidException(packFile, invalidatingCause);
 			}
 			if (length < pos + size)
 				size = (int) (length - pos);
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 94b9ddc188..f37c310752 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/IndexDiff.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/IndexDiff.java
@@ -47,7 +47,11 @@
 
 package org.eclipse.jgit.lib;
 
+import java.io.File;
 import java.io.IOException;
+import java.nio.file.DirectoryIteratorException;
+import java.nio.file.DirectoryStream;
+import java.nio.file.Files;
 import java.text.MessageFormat;
 import java.util.ArrayList;
 import java.util.Collection;
@@ -261,6 +265,8 @@ public class IndexDiff {
 
 	private Set<String> missing = new HashSet<>();
 
+	private Set<String> missingSubmodules = new HashSet<>();
+
 	private Set<String> modified = new HashSet<>();
 
 	private Set<String> untracked = new HashSet<>();
@@ -501,9 +507,15 @@ public class IndexDiff {
 				if (dirCacheIterator != null) {
 					if (workingTreeIterator == null) {
 						// in index, not in workdir => missing
-						if (!isEntryGitLink(dirCacheIterator)
-								|| ignoreSubmoduleMode != IgnoreSubmoduleMode.ALL)
-							missing.add(treeWalk.getPathString());
+						boolean isGitLink = isEntryGitLink(dirCacheIterator);
+						if (!isGitLink
+								|| ignoreSubmoduleMode != IgnoreSubmoduleMode.ALL) {
+							String path = treeWalk.getPathString();
+							missing.add(path);
+							if (isGitLink) {
+								missingSubmodules.add(path);
+							}
+						}
 					} else {
 						if (workingTreeIterator.isModified(
 								dirCacheIterator.getDirCacheEntry(), true,
@@ -543,8 +555,8 @@ public class IndexDiff {
 							smw.getPath()), e);
 				}
 				try (Repository subRepo = smw.getRepository()) {
+					String subRepoPath = smw.getPath();
 					if (subRepo != null) {
-						String subRepoPath = smw.getPath();
 						ObjectId subHead = subRepo.resolve("HEAD"); //$NON-NLS-1$
 						if (subHead != null
 								&& !subHead.equals(smw.getObjectId())) {
@@ -573,6 +585,21 @@ public class IndexDiff {
 								recordFileMode(subRepoPath, FileMode.GITLINK);
 							}
 						}
+					} else if (missingSubmodules.remove(subRepoPath)) {
+						// If the directory is there and empty but the submodule
+						// repository in .git/modules doesn't exist yet it isn't
+						// "missing".
+						File gitDir = new File(
+								new File(repository.getDirectory(),
+										Constants.MODULES),
+								subRepoPath);
+						if (!gitDir.isDirectory()) {
+							File dir = SubmoduleWalk.getSubmoduleDirectory(
+									repository, subRepoPath);
+							if (dir.isDirectory() && !hasFiles(dir)) {
+								missing.remove(subRepoPath);
+							}
+						}
 					}
 				}
 			}
@@ -592,6 +619,15 @@ public class IndexDiff {
 			return true;
 	}
 
+	private boolean hasFiles(File directory) {
+		try (DirectoryStream<java.nio.file.Path> dir = Files
+				.newDirectoryStream(directory.toPath())) {
+			return dir.iterator().hasNext();
+		} catch (DirectoryIteratorException | IOException e) {
+			return false;
+		}
+	}
+
 	private void recordFileMode(String path, FileMode mode) {
 		Set<String> values = fileModes.get(mode);
 		if (path != null) {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/util/Paths.java b/org.eclipse.jgit/src/org/eclipse/jgit/util/Paths.java
index be1b95e0d4..6be7ddbe12 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/util/Paths.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/util/Paths.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (C) 2016, 2018 Google Inc.
+ * Copyright (C) 2016, Google Inc.
  * and other copyright owners as documented in the project's IP log.
  *
  * This program and the accompanying materials are made available
@@ -43,7 +43,6 @@
 
 package org.eclipse.jgit.util;
 
-import static org.eclipse.jgit.lib.FileMode.TYPE_GITLINK;
 import static org.eclipse.jgit.lib.FileMode.TYPE_MASK;
 import static org.eclipse.jgit.lib.FileMode.TYPE_TREE;
 
@@ -107,7 +106,7 @@ public class Paths {
 				aPath, aPos, aEnd, aMode,
 				bPath, bPos, bEnd, bMode);
 		if (cmp == 0) {
-			cmp = modeCompare(aMode, bMode);
+			cmp = lastPathChar(aMode) - lastPathChar(bMode);
 		}
 		return cmp;
 	}
@@ -184,15 +183,6 @@ public class Paths {
 		return 0;
 	}
 
-	private static int modeCompare(int aMode, int bMode) {
-		if ((aMode & TYPE_MASK) == TYPE_GITLINK
-				|| (bMode & TYPE_MASK) == TYPE_GITLINK) {
-			// Git links can be equal to files or folders
-			return 0;
-		}
-		return lastPathChar(aMode) - lastPathChar(bMode);
-	}
-
 	private Paths() {
 	}
 }