Merge branch 'stable-5.4' into stable-5.5

* stable-5.4:
  Fix string format parameter for invalidRefAdvertisementLine
  WindowCache: add metric for cached bytes per repository
  pgm daemon: fallback to user and system config if no config specified
  WindowCache: add option to use strong refs to reference ByteWindows
  Replace usage of ArrayIndexOutOfBoundsException in treewalk
  Add config constants for WindowCache configuration options

Change-Id: I76a62da98182f0c504b1ea8b7d37cecdf4eea7e0

10 files changed, 540 insertions, 115 deletions

diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Daemon.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Daemon.java
index 43826636aa..8b86c16884 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Daemon.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Daemon.java
@@ -44,6 +44,7 @@
 package org.eclipse.jgit.pgm;
 
 import java.io.File;
+import java.io.IOException;
 import java.net.InetSocketAddress;
 import java.net.URISyntaxException;
 import java.text.MessageFormat;
@@ -51,12 +52,14 @@ import java.util.ArrayList;
 import java.util.List;
 import java.util.concurrent.Executors;
 
+import org.eclipse.jgit.errors.ConfigInvalidException;
 import org.eclipse.jgit.internal.ketch.KetchLeader;
 import org.eclipse.jgit.internal.ketch.KetchLeaderCache;
 import org.eclipse.jgit.internal.ketch.KetchPreReceive;
 import org.eclipse.jgit.internal.ketch.KetchSystem;
 import org.eclipse.jgit.internal.ketch.KetchText;
 import org.eclipse.jgit.lib.Repository;
+import org.eclipse.jgit.lib.StoredConfig;
 import org.eclipse.jgit.pgm.internal.CLIText;
 import org.eclipse.jgit.storage.file.FileBasedConfig;
 import org.eclipse.jgit.storage.file.WindowCacheConfig;
@@ -68,6 +71,7 @@ import org.eclipse.jgit.transport.resolver.FileResolver;
 import org.eclipse.jgit.transport.resolver.ReceivePackFactory;
 import org.eclipse.jgit.transport.resolver.ServiceNotEnabledException;
 import org.eclipse.jgit.util.FS;
+import org.eclipse.jgit.util.SystemReader;
 import org.kohsuke.args4j.Argument;
 import org.kohsuke.args4j.Option;
 
@@ -120,19 +124,20 @@ class Daemon extends TextBuiltin {
 	@Override
 	protected void run() throws Exception {
 		PackConfig packConfig = new PackConfig();
-
-		if (configFile != null) {
+		StoredConfig cfg;
+		if (configFile == null) {
+			cfg = getUserConfig();
+		} else {
 			if (!configFile.exists()) {
 				throw die(MessageFormat.format(
 						CLIText.get().configFileNotFound, //
 						configFile.getAbsolutePath()));
 			}
-
-			FileBasedConfig cfg = new FileBasedConfig(configFile, FS.DETECTED);
-			cfg.load();
-			new WindowCacheConfig().fromConfig(cfg).install();
-			packConfig.fromConfig(cfg);
+			cfg = new FileBasedConfig(configFile, FS.DETECTED);
 		}
+		cfg.load();
+		new WindowCacheConfig().fromConfig(cfg).install();
+		packConfig.fromConfig(cfg);
 
 		int threads = packConfig.getThreads();
 		if (threads <= 0)
@@ -172,6 +177,16 @@ class Daemon extends TextBuiltin {
 		outw.println(MessageFormat.format(CLIText.get().listeningOn, d.getAddress()));
 	}
 
+	private StoredConfig getUserConfig() throws IOException {
+		StoredConfig userConfig = null;
+		try {
+			userConfig = SystemReader.getInstance().getUserConfig();
+		} catch (ConfigInvalidException e) {
+			throw die(e.getMessage());
+		}
+		return userConfig;
+	}
+
 	private static DaemonService service(
 			final org.eclipse.jgit.transport.Daemon d,
 			final String n) {
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/WindowCacheGetTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/WindowCacheGetTest.java
index f1a18b096c..a173532db1 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/WindowCacheGetTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/WindowCacheGetTest.java
@@ -53,6 +53,8 @@ import java.io.FileInputStream;
 import java.io.IOException;
 import java.io.InputStreamReader;
 import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
 import java.util.List;
 
 import org.eclipse.jgit.errors.CorruptObjectException;
@@ -66,9 +68,25 @@ import org.eclipse.jgit.test.resources.SampleDataRepositoryTestCase;
 import org.eclipse.jgit.util.MutableInteger;
 import org.junit.Before;
 import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.junit.runners.Parameterized;
+import org.junit.runners.Parameterized.Parameters;
 
+@RunWith(Parameterized.class)
 public class WindowCacheGetTest extends SampleDataRepositoryTestCase {
 	private List<TestObject> toLoad;
+	private WindowCacheConfig cfg;
+	private boolean useStrongRefs;
+
+	@Parameters(name = "useStrongRefs={0}")
+	public static Collection<Object[]> data() {
+		return Arrays
+				.asList(new Object[][] { { Boolean.TRUE }, { Boolean.FALSE } });
+	}
+
+	public WindowCacheGetTest(Boolean useStrongRef) {
+		this.useStrongRefs = useStrongRef.booleanValue();
+	}
 
 	@Override
 	@Before
@@ -93,11 +111,12 @@ public class WindowCacheGetTest extends SampleDataRepositoryTestCase {
 			}
 		}
 		assertEquals(96, toLoad.size());
+		cfg = new WindowCacheConfig();
+		cfg.setPackedGitUseStrongRefs(useStrongRefs);
 	}
 
 	@Test
 	public void testCache_Defaults() throws IOException {
-		WindowCacheConfig cfg = new WindowCacheConfig();
 		cfg.install();
 		doCacheTests();
 		checkLimits(cfg);
@@ -122,7 +141,6 @@ public class WindowCacheGetTest extends SampleDataRepositoryTestCase {
 
 	@Test
 	public void testCache_TooFewFiles() throws IOException {
-		final WindowCacheConfig cfg = new WindowCacheConfig();
 		cfg.setPackedGitOpenFiles(2);
 		cfg.install();
 		doCacheTests();
@@ -131,7 +149,6 @@ public class WindowCacheGetTest extends SampleDataRepositoryTestCase {
 
 	@Test
 	public void testCache_TooSmallLimit() throws IOException {
-		final WindowCacheConfig cfg = new WindowCacheConfig();
 		cfg.setPackedGitWindowSize(4096);
 		cfg.setPackedGitLimit(4096);
 		cfg.install();
@@ -142,26 +159,31 @@ public class WindowCacheGetTest extends SampleDataRepositoryTestCase {
 	private static void checkLimits(WindowCacheConfig cfg) {
 		final WindowCache cache = WindowCache.getInstance();
 		WindowCacheStats s = cache.getStats();
-		assertTrue(0 < s.getAverageLoadTime());
-		assertTrue(0 < s.getOpenByteCount());
-		assertTrue(0 < s.getOpenByteCount());
-		assertTrue(0.0 < s.getAverageLoadTime());
-		assertTrue(0 <= s.getEvictionCount());
-		assertTrue(0 < s.getHitCount());
-		assertTrue(0 < s.getHitRatio());
-		assertTrue(1 > s.getHitRatio());
-		assertTrue(0 < s.getLoadCount());
-		assertTrue(0 <= s.getLoadFailureCount());
-		assertTrue(0.0 <= s.getLoadFailureRatio());
-		assertTrue(1 > s.getLoadFailureRatio());
-		assertTrue(0 < s.getLoadSuccessCount());
-		assertTrue(s.getOpenByteCount() <= cfg.getPackedGitLimit());
-		assertTrue(s.getOpenFileCount() <= cfg.getPackedGitOpenFiles());
-		assertTrue(0 <= s.getMissCount());
-		assertTrue(0 <= s.getMissRatio());
-		assertTrue(1 > s.getMissRatio());
-		assertTrue(0 < s.getRequestCount());
-		assertTrue(0 < s.getTotalLoadTime());
+		assertTrue("average load time should be > 0",
+				0 < s.getAverageLoadTime());
+		assertTrue("open byte count should be > 0", 0 < s.getOpenByteCount());
+		assertTrue("eviction count should be >= 0", 0 <= s.getEvictionCount());
+		assertTrue("hit count should be > 0", 0 < s.getHitCount());
+		assertTrue("hit ratio should be > 0", 0 < s.getHitRatio());
+		assertTrue("hit ratio should be < 1", 1 > s.getHitRatio());
+		assertTrue("load count should be > 0", 0 < s.getLoadCount());
+		assertTrue("load failure count should be >= 0",
+				0 <= s.getLoadFailureCount());
+		assertTrue("load failure ratio should be >= 0",
+				0.0 <= s.getLoadFailureRatio());
+		assertTrue("load failure ratio should be < 1",
+				1 > s.getLoadFailureRatio());
+		assertTrue("load success count should be > 0",
+				0 < s.getLoadSuccessCount());
+		assertTrue("open byte count should be <= core.packedGitLimit",
+				s.getOpenByteCount() <= cfg.getPackedGitLimit());
+		assertTrue("open file count should be <= core.packedGitOpenFiles",
+				s.getOpenFileCount() <= cfg.getPackedGitOpenFiles());
+		assertTrue("miss success count should be >= 0", 0 <= s.getMissCount());
+		assertTrue("miss ratio should be > 0", 0 <= s.getMissRatio());
+		assertTrue("miss ratio should be < 1", 1 > s.getMissRatio());
+		assertTrue("request count should be > 0", 0 < s.getRequestCount());
+		assertTrue("total load time should be > 0", 0 < s.getTotalLoadTime());
 	}
 
 	private void doCacheTests() throws IOException {
diff --git a/org.eclipse.jgit/.settings/.api_filters b/org.eclipse.jgit/.settings/.api_filters
index 58ec3cb418..a2066ec3ed 100644
--- a/org.eclipse.jgit/.settings/.api_filters
+++ b/org.eclipse.jgit/.settings/.api_filters
@@ -1,13 +1,5 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <component id="org.eclipse.jgit" version="2">
-    <resource path="META-INF/MANIFEST.MF">
-        <filter id="924844039">
-            <message_arguments>
-                <message_argument value="5.5.2"/>
-                <message_argument value="5.5.0"/>
-            </message_arguments>
-        </filter>
-    </resource>
     <resource path="src/org/eclipse/jgit/dircache/DirCacheEntry.java" type="org.eclipse.jgit.dircache.DirCacheEntry">
         <filter id="1142947843">
             <message_arguments>
@@ -54,6 +46,36 @@
         </filter>
         <filter id="1142947843">
             <message_arguments>
+                <message_argument value="5.1.13"/>
+                <message_argument value="CONFIG_KEY_PACKED_GIT_LIMIT"/>
+            </message_arguments>
+        </filter>
+        <filter id="1142947843">
+            <message_arguments>
+                <message_argument value="5.1.13"/>
+                <message_argument value="CONFIG_KEY_PACKED_GIT_MMAP"/>
+            </message_arguments>
+        </filter>
+        <filter id="1142947843">
+            <message_arguments>
+                <message_argument value="5.1.13"/>
+                <message_argument value="CONFIG_KEY_PACKED_GIT_OPENFILES"/>
+            </message_arguments>
+        </filter>
+        <filter id="1142947843">
+            <message_arguments>
+                <message_argument value="5.1.13"/>
+                <message_argument value="CONFIG_KEY_PACKED_GIT_USE_STRONGREFS"/>
+            </message_arguments>
+        </filter>
+        <filter id="1142947843">
+            <message_arguments>
+                <message_argument value="5.1.13"/>
+                <message_argument value="CONFIG_KEY_PACKED_GIT_WINDOWSIZE"/>
+            </message_arguments>
+        </filter>
+        <filter id="1142947843">
+            <message_arguments>
                 <message_argument value="5.1.9"/>
                 <message_argument value="CONFIG_FILESYSTEM_SECTION"/>
             </message_arguments>
@@ -79,6 +101,20 @@
             </message_arguments>
         </filter>
     </resource>
+    <resource path="src/org/eclipse/jgit/storage/file/WindowCacheConfig.java" type="org.eclipse.jgit.storage.file.WindowCacheConfig">
+        <filter id="1142947843">
+            <message_arguments>
+                <message_argument value="5.1.13"/>
+                <message_argument value="isPackedGitUseStrongRefs()"/>
+            </message_arguments>
+        </filter>
+        <filter id="1142947843">
+            <message_arguments>
+                <message_argument value="5.1.13"/>
+                <message_argument value="setPackedGitUseStrongRefs(boolean)"/>
+            </message_arguments>
+        </filter>
+    </resource>
     <resource path="src/org/eclipse/jgit/storage/file/WindowCacheStats.java" type="org.eclipse.jgit.storage.file.WindowCacheStats">
         <filter id="337809484">
             <message_arguments>
diff --git a/org.eclipse.jgit/resources/org/eclipse/jgit/internal/JGitText.properties b/org.eclipse.jgit/resources/org/eclipse/jgit/internal/JGitText.properties
index b82512f71b..52359d1f12 100644
--- a/org.eclipse.jgit/resources/org/eclipse/jgit/internal/JGitText.properties
+++ b/org.eclipse.jgit/resources/org/eclipse/jgit/internal/JGitText.properties
@@ -368,7 +368,7 @@ invalidPacketLineHeader=Invalid packet line header: {0}
 invalidPath=Invalid path: {0}
 invalidPurgeFactor=Invalid purgeFactor {0}, values have to be in range between 0 and 1
 invalidRedirectLocation=Invalid redirect location {0} -> {1}
-invalidRefAdvertisementLine=Invalid ref advertisement line: ''{1}''
+invalidRefAdvertisementLine=Invalid ref advertisement line: ''{0}''
 invalidReflogRevision=Invalid reflog revision: {0}
 invalidRefName=Invalid ref name: {0}
 invalidReftableBlock=Invalid reftable block
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/WindowCache.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/WindowCache.java
index 015866e101..838de0b336 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/WindowCache.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/WindowCache.java
@@ -47,11 +47,16 @@ package org.eclipse.jgit.internal.storage.file;
 import java.io.IOException;
 import java.lang.ref.ReferenceQueue;
 import java.lang.ref.SoftReference;
+import java.util.Collections;
+import java.util.Map;
 import java.util.Random;
+import java.util.concurrent.ConcurrentHashMap;
+import java.util.concurrent.ConcurrentLinkedQueue;
 import java.util.concurrent.atomic.AtomicLong;
 import java.util.concurrent.atomic.AtomicReferenceArray;
 import java.util.concurrent.atomic.LongAdder;
 import java.util.concurrent.locks.ReentrantLock;
+import java.util.stream.Collectors;
 
 import org.eclipse.jgit.annotations.NonNull;
 import org.eclipse.jgit.internal.JGitText;
@@ -85,9 +90,16 @@ import org.eclipse.jgit.util.Monitoring;
  * comprised of roughly 10% of the cache, and evicting the oldest accessed entry
  * within that window.
  * <p>
- * Entities created by the cache are held under SoftReferences, permitting the
+ * Entities created by the cache are held under SoftReferences if option
+ * {@code core.packedGitUseStrongRefs} is set to {@code false} in the git config
+ * (this is the default) or by calling
+ * {@link WindowCacheConfig#setPackedGitUseStrongRefs(boolean)}, permitting the
  * Java runtime's garbage collector to evict entries when heap memory gets low.
  * Most JREs implement a loose least recently used algorithm for this eviction.
+ * When this option is set to {@code true} strong references are used which
+ * means that Java gc cannot evict the WindowCache to reclaim memory. On the
+ * other hand this provides more predictable performance since the cache isn't
+ * flushed when used heap comes close to the maximum heap size.
  * <p>
  * The internal hash table does not expand at runtime, instead it is fixed in
  * size at cache creation time. The internal lock table used to gate load
@@ -104,19 +116,19 @@ import org.eclipse.jgit.util.Monitoring;
  * for a given <code>(PackFile,position)</code> tuple.</li>
  * <li>For every <code>load()</code> invocation there is exactly one
  * {@link #createRef(PackFile, long, ByteWindow)} invocation to wrap a
- * SoftReference around the cached entity.</li>
+ * SoftReference or a StrongReference around the cached entity.</li>
  * <li>For every Reference created by <code>createRef()</code> there will be
- * exactly one call to {@link #clear(Ref)} to cleanup any resources associated
+ * exactly one call to {@link #clear(PageRef)} to cleanup any resources associated
  * with the (now expired) cached entity.</li>
  * </ul>
  * <p>
  * Therefore, it is safe to perform resource accounting increments during the
  * {@link #load(PackFile, long)} or
  * {@link #createRef(PackFile, long, ByteWindow)} methods, and matching
- * decrements during {@link #clear(Ref)}. Implementors may need to override
+ * decrements during {@link #clear(PageRef)}. Implementors may need to override
  * {@link #createRef(PackFile, long, ByteWindow)} in order to embed additional
  * accounting information into an implementation specific
- * {@link org.eclipse.jgit.internal.storage.file.WindowCache.Ref} subclass, as
+ * {@link org.eclipse.jgit.internal.storage.file.WindowCache.PageRef} subclass, as
  * the cached entity may have already been evicted by the JRE's garbage
  * collector.
  * <p>
@@ -176,18 +188,21 @@ public class WindowCache {
 		/**
 		 * Record files opened by cache
 		 *
-		 * @param count
+		 * @param delta
 		 *            delta of number of files opened by cache
 		 */
-		void recordOpenFiles(int count);
+		void recordOpenFiles(int delta);
 
 		/**
 		 * Record cached bytes
 		 *
-		 * @param count
+		 * @param pack
+		 *            pack file the bytes are read from
+		 *
+		 * @param delta
 		 *            delta of cached bytes
 		 */
-		void recordOpenBytes(int count);
+		void recordOpenBytes(PackFile pack, int delta);
 
 		/**
 		 * Returns a snapshot of this recorder's stats. Note that this may be an
@@ -209,6 +224,7 @@ public class WindowCache {
 		private final LongAdder evictionCount;
 		private final LongAdder openFileCount;
 		private final LongAdder openByteCount;
+		private final Map<String, LongAdder> openByteCountPerRepository;
 
 		/**
 		 * Constructs an instance with all counts initialized to zero.
@@ -222,6 +238,7 @@ public class WindowCache {
 			evictionCount = new LongAdder();
 			openFileCount = new LongAdder();
 			openByteCount = new LongAdder();
+			openByteCountPerRepository = new ConcurrentHashMap<>();
 		}
 
 		@Override
@@ -252,13 +269,28 @@ public class WindowCache {
 		}
 
 		@Override
-		public void recordOpenFiles(int count) {
-			openFileCount.add(count);
+		public void recordOpenFiles(int delta) {
+			openFileCount.add(delta);
 		}
 
 		@Override
-		public void recordOpenBytes(int count) {
-			openByteCount.add(count);
+		public void recordOpenBytes(PackFile pack, int delta) {
+			openByteCount.add(delta);
+			String repositoryId = repositoryId(pack);
+			LongAdder la = openByteCountPerRepository
+					.computeIfAbsent(repositoryId, k -> new LongAdder());
+			la.add(delta);
+			if (delta < 0) {
+				openByteCountPerRepository.computeIfPresent(repositoryId,
+						(k, v) -> v.longValue() == 0 ? null : v);
+			}
+		}
+
+		private static String repositoryId(PackFile pack) {
+			// use repository's gitdir since packfile doesn't know its
+			// repository
+			return pack.getPackFile().getParentFile().getParentFile()
+					.getParent();
 		}
 
 		@Override
@@ -315,6 +347,15 @@ public class WindowCache {
 			totalLoadTime.reset();
 			evictionCount.reset();
 		}
+
+		@Override
+		public Map<String, Long> getOpenByteCountPerRepository() {
+			return Collections.unmodifiableMap(
+					openByteCountPerRepository.entrySet().stream()
+							.collect(Collectors.toMap(Map.Entry::getKey,
+									e -> Long.valueOf(e.getValue().sum()),
+									(u, v) -> v)));
+		}
 	}
 
 	private static final int bits(int newSize) {
@@ -390,8 +431,8 @@ public class WindowCache {
 		cache.removeAll(pack);
 	}
 
-	/** ReferenceQueue to cleanup released and garbage collected windows. */
-	private final ReferenceQueue<ByteWindow> queue;
+	/** cleanup released and/or garbage collected windows. */
+	private final CleanupQueue queue;
 
 	/** Number of entries in {@link #table}. */
 	private final int tableSize;
@@ -425,6 +466,8 @@ public class WindowCache {
 
 	private final StatsRecorderImpl mbean;
 
+	private boolean useStrongRefs;
+
 	private WindowCache(WindowCacheConfig cfg) {
 		tableSize = tableSize(cfg);
 		final int lockCount = lockCount(cfg);
@@ -433,7 +476,6 @@ public class WindowCache {
 		if (lockCount < 1)
 			throw new IllegalArgumentException(JGitText.get().lockCountMustBeGreaterOrEqual1);
 
-		queue = new ReferenceQueue<>();
 		clock = new AtomicLong(1);
 		table = new AtomicReferenceArray<>(tableSize);
 		locks = new Lock[lockCount];
@@ -455,6 +497,9 @@ public class WindowCache {
 		mmap = cfg.isPackedGitMMAP();
 		windowSizeShift = bits(cfg.getPackedGitWindowSize());
 		windowSize = 1 << windowSizeShift;
+		useStrongRefs = cfg.isPackedGitUseStrongRefs();
+		queue = useStrongRefs ? new StrongCleanupQueue(this)
+				: new SoftCleanupQueue(this);
 
 		mbean = new StatsRecorderImpl();
 		statsRecorder = mbean;
@@ -503,16 +548,18 @@ public class WindowCache {
 		}
 	}
 
-	private Ref createRef(PackFile p, long o, ByteWindow v) {
-		final Ref ref = new Ref(p, o, v, queue);
-		statsRecorder.recordOpenBytes(ref.size);
+	private PageRef<ByteWindow> createRef(PackFile p, long o, ByteWindow v) {
+		final PageRef<ByteWindow> ref = useStrongRefs
+				? new StrongRef(p, o, v, queue)
+				: new SoftRef(p, o, v, (SoftCleanupQueue) queue);
+		statsRecorder.recordOpenBytes(ref.getPack(), ref.getSize());
 		return ref;
 	}
 
-	private void clear(Ref ref) {
-		statsRecorder.recordOpenBytes(-ref.size);
+	private void clear(PageRef<ByteWindow> ref) {
+		statsRecorder.recordOpenBytes(ref.getPack(), -ref.getSize());
 		statsRecorder.recordEvictions(1);
-		close(ref.pack);
+		close(ref.getPack());
 	}
 
 	private void close(PackFile pack) {
@@ -577,7 +624,7 @@ public class WindowCache {
 			}
 
 			v = load(pack, position);
-			final Ref ref = createRef(pack, position, v);
+			final PageRef<ByteWindow> ref = createRef(pack, position, v);
 			hit(ref);
 			for (;;) {
 				final Entry n = new Entry(clean(e2), ref);
@@ -601,8 +648,8 @@ public class WindowCache {
 
 	private ByteWindow scan(Entry n, PackFile pack, long position) {
 		for (; n != null; n = n.next) {
-			final Ref r = n.ref;
-			if (r.pack == pack && r.position == position) {
+			final PageRef<ByteWindow> r = n.ref;
+			if (r.getPack() == pack && r.getPosition() == position) {
 				final ByteWindow v = r.get();
 				if (v != null) {
 					hit(r);
@@ -615,7 +662,7 @@ public class WindowCache {
 		return null;
 	}
 
-	private void hit(Ref r) {
+	private void hit(PageRef r) {
 		// We don't need to be 100% accurate here. Its sufficient that at least
 		// one thread performs the increment. Any other concurrent access at
 		// exactly the same time can simply use the same clock value.
@@ -625,7 +672,7 @@ public class WindowCache {
 		//
 		final long c = clock.get();
 		clock.compareAndSet(c, c + 1);
-		r.lastAccess = c;
+		r.setLastAccess(c);
 	}
 
 	private void evict() {
@@ -639,7 +686,8 @@ public class WindowCache {
 				for (Entry e = table.get(ptr); e != null; e = e.next) {
 					if (e.dead)
 						continue;
-					if (old == null || e.ref.lastAccess < old.ref.lastAccess) {
+					if (old == null || e.ref.getLastAccess() < old.ref
+							.getLastAccess()) {
 						old = e;
 						slot = ptr;
 					}
@@ -659,7 +707,7 @@ public class WindowCache {
 	 * <p>
 	 * This is a last-ditch effort to clear out the cache, such as before it
 	 * gets replaced by another cache that is configured differently. This
-	 * method tries to force every cached entry through {@link #clear(Ref)} to
+	 * method tries to force every cached entry through {@link #clear(PageRef)} to
 	 * ensure that resources are correctly accounted for and cleaned up by the
 	 * subclass. A concurrent reader loading entries while this method is
 	 * running may cause resource accounting failures.
@@ -692,7 +740,7 @@ public class WindowCache {
 			final Entry e1 = table.get(s);
 			boolean hasDead = false;
 			for (Entry e = e1; e != null; e = e.next) {
-				if (e.ref.pack == pack) {
+				if (e.ref.getPack() == pack) {
 					e.kill();
 					hasDead = true;
 				} else if (e.dead)
@@ -705,20 +753,7 @@ public class WindowCache {
 	}
 
 	private void gc() {
-		Ref r;
-		while ((r = (Ref) queue.poll()) != null) {
-			clear(r);
-
-			final int s = slot(r.pack, r.position);
-			final Entry e1 = table.get(s);
-			for (Entry n = e1; n != null; n = n.next) {
-				if (n.ref == r) {
-					n.dead = true;
-					table.compareAndSet(s, e1, clean(e1));
-					break;
-				}
-			}
-		}
+		queue.gc();
 	}
 
 	private int slot(PackFile pack, long position) {
@@ -731,7 +766,7 @@ public class WindowCache {
 
 	private static Entry clean(Entry top) {
 		while (top != null && top.dead) {
-			top.ref.enqueue();
+			top.ref.kill();
 			top = top.next;
 		}
 		if (top == null)
@@ -745,7 +780,7 @@ public class WindowCache {
 		final Entry next;
 
 		/** The referenced object. */
-		final Ref ref;
+		final PageRef<ByteWindow> ref;
 
 		/**
 		 * Marked true when ref.get() returns null and the ref is dead.
@@ -756,34 +791,275 @@ public class WindowCache {
 		 */
 		volatile boolean dead;
 
-		Entry(Entry n, Ref r) {
+		Entry(Entry n, PageRef<ByteWindow> r) {
 			next = n;
 			ref = r;
 		}
 
 		final void kill() {
 			dead = true;
-			ref.enqueue();
+			ref.kill();
 		}
 	}
 
+	private static interface PageRef<T> {
+		/**
+		 * Returns this reference object's referent. If this reference object
+		 * has been cleared, either by the program or by the garbage collector,
+		 * then this method returns <code>null</code>.
+		 *
+		 * @return The object to which this reference refers, or
+		 *         <code>null</code> if this reference object has been cleared
+		 */
+		T get();
+
+	    /**
+		 * Kill this ref
+		 *
+		 * @return <code>true</code> if this reference object was successfully
+		 *         killed; <code>false</code> if it was already killed
+		 */
+		boolean kill();
+
+		/**
+		 * Get the packfile the referenced cache page is allocated for
+		 *
+		 * @return the packfile the referenced cache page is allocated for
+		 */
+		PackFile getPack();
+
+		/**
+		 * Get the position of the referenced cache page in the packfile
+		 *
+		 * @return the position of the referenced cache page in the packfile
+		 */
+		long getPosition();
+
+		/**
+		 * Get size of cache page
+		 *
+		 * @return size of cache page
+		 */
+		int getSize();
+
+		/**
+		 * Get pseudo time of last access to this cache page
+		 *
+		 * @return pseudo time of last access to this cache page
+		 */
+		long getLastAccess();
+
+		/**
+		 * Set pseudo time of last access to this cache page
+		 *
+		 * @param time
+		 *            pseudo time of last access to this cache page
+		 */
+		void setLastAccess(long time);
+
+		/**
+		 * Whether this is a strong reference.
+		 * @return {@code true} if this is a strong reference
+		 */
+		boolean isStrongRef();
+	}
+
 	/** A soft reference wrapped around a cached object. */
-	private static class Ref extends SoftReference<ByteWindow> {
-		final PackFile pack;
+	private static class SoftRef extends SoftReference<ByteWindow>
+			implements PageRef<ByteWindow> {
+		private final PackFile pack;
 
-		final long position;
+		private final long position;
 
-		final int size;
+		private final int size;
 
-		long lastAccess;
+		private long lastAccess;
 
-		protected Ref(final PackFile pack, final long position,
-				final ByteWindow v, final ReferenceQueue<ByteWindow> queue) {
+		protected SoftRef(final PackFile pack, final long position,
+				final ByteWindow v, final SoftCleanupQueue queue) {
 			super(v, queue);
 			this.pack = pack;
 			this.position = position;
 			this.size = v.size();
 		}
+
+		@Override
+		public PackFile getPack() {
+			return pack;
+		}
+
+		@Override
+		public long getPosition() {
+			return position;
+		}
+
+		@Override
+		public int getSize() {
+			return size;
+		}
+
+		@Override
+		public long getLastAccess() {
+			return lastAccess;
+		}
+
+		@Override
+		public void setLastAccess(long time) {
+			this.lastAccess = time;
+		}
+
+		@Override
+		public boolean kill() {
+			return enqueue();
+		}
+
+		@Override
+		public boolean isStrongRef() {
+			return false;
+		}
+	}
+
+	/** A strong reference wrapped around a cached object. */
+	private static class StrongRef implements PageRef<ByteWindow> {
+		private ByteWindow referent;
+
+		private final PackFile pack;
+
+		private final long position;
+
+		private final int size;
+
+		private long lastAccess;
+
+		private CleanupQueue queue;
+
+		protected StrongRef(final PackFile pack, final long position,
+				final ByteWindow v, final CleanupQueue queue) {
+			this.pack = pack;
+			this.position = position;
+			this.referent = v;
+			this.size = v.size();
+			this.queue = queue;
+		}
+
+		@Override
+		public PackFile getPack() {
+			return pack;
+		}
+
+		@Override
+		public long getPosition() {
+			return position;
+		}
+
+		@Override
+		public int getSize() {
+			return size;
+		}
+
+		@Override
+		public long getLastAccess() {
+			return lastAccess;
+		}
+
+		@Override
+		public void setLastAccess(long time) {
+			this.lastAccess = time;
+		}
+
+		@Override
+		public ByteWindow get() {
+			return referent;
+		}
+
+		@Override
+		public boolean kill() {
+			if (referent == null) {
+				return false;
+			}
+			referent = null;
+			return queue.enqueue(this);
+		}
+
+		@Override
+		public boolean isStrongRef() {
+			return true;
+		}
+	}
+
+	private static interface CleanupQueue {
+		boolean enqueue(PageRef<ByteWindow> r);
+		void gc();
+	}
+
+	private static class SoftCleanupQueue extends ReferenceQueue<ByteWindow>
+			implements CleanupQueue {
+		private final WindowCache wc;
+
+		SoftCleanupQueue(WindowCache cache) {
+			this.wc = cache;
+		}
+
+		@Override
+		public boolean enqueue(PageRef<ByteWindow> r) {
+			// no need to explicitly add soft references which are enqueued by
+			// the JVM
+			return false;
+		}
+
+		@Override
+		public void gc() {
+			SoftRef r;
+			while ((r = (SoftRef) poll()) != null) {
+				wc.clear(r);
+
+				final int s = wc.slot(r.getPack(), r.getPosition());
+				final Entry e1 = wc.table.get(s);
+				for (Entry n = e1; n != null; n = n.next) {
+					if (n.ref == r) {
+						n.dead = true;
+						wc.table.compareAndSet(s, e1, clean(e1));
+						break;
+					}
+				}
+			}
+		}
+	}
+
+	private static class StrongCleanupQueue implements CleanupQueue {
+		private final WindowCache wc;
+
+		private final ConcurrentLinkedQueue<PageRef<ByteWindow>> queue = new ConcurrentLinkedQueue<>();
+
+		StrongCleanupQueue(WindowCache wc) {
+			this.wc = wc;
+		}
+
+		@Override
+		public boolean enqueue(PageRef<ByteWindow> r) {
+			if (queue.contains(r)) {
+				return false;
+			}
+			return queue.add(r);
+		}
+
+		@Override
+		public void gc() {
+			PageRef<ByteWindow> r;
+			while ((r = queue.poll()) != null) {
+				wc.clear(r);
+
+				final int s = wc.slot(r.getPack(), r.getPosition());
+				final Entry e1 = wc.table.get(s);
+				for (Entry n = e1; n != null; n = n.next) {
+					if (n.ref == r) {
+						n.dead = true;
+						wc.table.compareAndSet(s, e1, clean(e1));
+						break;
+					}
+				}
+			}
+		}
 	}
 
 	private static final class Lock {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/ConfigConstants.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/ConfigConstants.java
index 068a8d82e6..078bf786f2 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/ConfigConstants.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/ConfigConstants.java
@@ -230,6 +230,36 @@ public final class ConfigConstants {
 	/** The "streamFileThreshold" key */
 	public static final String CONFIG_KEY_STREAM_FILE_TRESHOLD = "streamFileThreshold";
 
+	/**
+	 * The "packedGitMmap" key
+	 * @since 5.1.13
+	 */
+	public static final String CONFIG_KEY_PACKED_GIT_MMAP = "packedgitmmap";
+
+	/**
+	 * The "packedGitWindowSize" key
+	 * @since 5.1.13
+	 */
+	public static final String CONFIG_KEY_PACKED_GIT_WINDOWSIZE = "packedgitwindowsize";
+
+	/**
+	 * The "packedGitLimit" key
+	 * @since 5.1.13
+	 */
+	public static final String CONFIG_KEY_PACKED_GIT_LIMIT = "packedgitlimit";
+
+	/**
+	 * The "packedGitOpenFiles" key
+	 * @since 5.1.13
+	 */
+	public static final String CONFIG_KEY_PACKED_GIT_OPENFILES = "packedgitopenfiles";
+
+	/**
+	 * The "packedGitUseStrongRefs" key
+	 * @since 5.1.13
+	 */
+	public static final String CONFIG_KEY_PACKED_GIT_USE_STRONGREFS = "packedgitusestrongrefs";
+
 	/** The "remote" key */
 	public static final String CONFIG_KEY_REMOTE = "remote";
 
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/storage/file/WindowCacheConfig.java b/org.eclipse.jgit/src/org/eclipse/jgit/storage/file/WindowCacheConfig.java
index ff499764c9..be19df82b2 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/storage/file/WindowCacheConfig.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/storage/file/WindowCacheConfig.java
@@ -43,6 +43,15 @@
 
 package org.eclipse.jgit.storage.file;
 
+import static org.eclipse.jgit.lib.ConfigConstants.CONFIG_CORE_SECTION;
+import static org.eclipse.jgit.lib.ConfigConstants.CONFIG_KEY_DELTA_BASE_CACHE_LIMIT;
+import static org.eclipse.jgit.lib.ConfigConstants.CONFIG_KEY_PACKED_GIT_LIMIT;
+import static org.eclipse.jgit.lib.ConfigConstants.CONFIG_KEY_PACKED_GIT_MMAP;
+import static org.eclipse.jgit.lib.ConfigConstants.CONFIG_KEY_PACKED_GIT_OPENFILES;
+import static org.eclipse.jgit.lib.ConfigConstants.CONFIG_KEY_PACKED_GIT_WINDOWSIZE;
+import static org.eclipse.jgit.lib.ConfigConstants.CONFIG_KEY_STREAM_FILE_TRESHOLD;
+import static org.eclipse.jgit.lib.ConfigConstants.CONFIG_KEY_PACKED_GIT_USE_STRONGREFS;
+
 import org.eclipse.jgit.internal.storage.file.WindowCache;
 import org.eclipse.jgit.lib.Config;
 import org.eclipse.jgit.storage.pack.PackConfig;
@@ -61,6 +70,8 @@ public class WindowCacheConfig {
 
 	private long packedGitLimit;
 
+	private boolean useStrongRefs;
+
 	private int packedGitWindowSize;
 
 	private boolean packedGitMMAP;
@@ -75,6 +86,7 @@ public class WindowCacheConfig {
 	public WindowCacheConfig() {
 		packedGitOpenFiles = 128;
 		packedGitLimit = 10 * MB;
+		useStrongRefs = false;
 		packedGitWindowSize = 8 * KB;
 		packedGitMMAP = false;
 		deltaBaseCacheLimit = 10 * MB;
@@ -126,6 +138,31 @@ public class WindowCacheConfig {
 	}
 
 	/**
+	 * Get whether the window cache should use strong references or
+	 * SoftReferences
+	 *
+	 * @return {@code true} if the window cache should use strong references,
+	 *         otherwise it will use {@link java.lang.ref.SoftReference}s
+	 * @since 5.1.13
+	 */
+	public boolean isPackedGitUseStrongRefs() {
+		return useStrongRefs;
+	}
+
+	/**
+	 * Set if the cache should use strong refs or soft refs
+	 *
+	 * @param useStrongRefs
+	 *            if @{code true} the cache strongly references cache pages
+	 *            otherwise it uses {@link java.lang.ref.SoftReference}s which
+	 *            can be evicted by the Java gc if heap is almost full
+	 * @since 5.1.13
+	 */
+	public void setPackedGitUseStrongRefs(boolean useStrongRefs) {
+		this.useStrongRefs = useStrongRefs;
+	}
+
+	/**
 	 * Get size in bytes of a single window mapped or read in from the pack
 	 * file.
 	 *
@@ -227,20 +264,23 @@ public class WindowCacheConfig {
 	 * @since 3.0
 	 */
 	public WindowCacheConfig fromConfig(Config rc) {
-		setPackedGitOpenFiles(rc.getInt(
-				"core", null, "packedgitopenfiles", getPackedGitOpenFiles())); //$NON-NLS-1$ //$NON-NLS-2$
-		setPackedGitLimit(rc.getLong(
-				"core", null, "packedgitlimit", getPackedGitLimit())); //$NON-NLS-1$ //$NON-NLS-2$
-		setPackedGitWindowSize(rc.getInt(
-				"core", null, "packedgitwindowsize", getPackedGitWindowSize())); //$NON-NLS-1$ //$NON-NLS-2$
-		setPackedGitMMAP(rc.getBoolean(
-				"core", null, "packedgitmmap", isPackedGitMMAP())); //$NON-NLS-1$ //$NON-NLS-2$
-		setDeltaBaseCacheLimit(rc.getInt(
-				"core", null, "deltabasecachelimit", getDeltaBaseCacheLimit())); //$NON-NLS-1$ //$NON-NLS-2$
+		setPackedGitUseStrongRefs(rc.getBoolean(CONFIG_CORE_SECTION,
+				CONFIG_KEY_PACKED_GIT_USE_STRONGREFS,
+				isPackedGitUseStrongRefs()));
+		setPackedGitOpenFiles(rc.getInt(CONFIG_CORE_SECTION, null,
+				CONFIG_KEY_PACKED_GIT_OPENFILES, getPackedGitOpenFiles()));
+		setPackedGitLimit(rc.getLong(CONFIG_CORE_SECTION, null,
+				CONFIG_KEY_PACKED_GIT_LIMIT, getPackedGitLimit()));
+		setPackedGitWindowSize(rc.getInt(CONFIG_CORE_SECTION, null,
+				CONFIG_KEY_PACKED_GIT_WINDOWSIZE, getPackedGitWindowSize()));
+		setPackedGitMMAP(rc.getBoolean(CONFIG_CORE_SECTION, null,
+				CONFIG_KEY_PACKED_GIT_MMAP, isPackedGitMMAP()));
+		setDeltaBaseCacheLimit(rc.getInt(CONFIG_CORE_SECTION, null,
+				CONFIG_KEY_DELTA_BASE_CACHE_LIMIT, getDeltaBaseCacheLimit()));
 
 		long maxMem = Runtime.getRuntime().maxMemory();
-		long sft = rc.getLong(
-				"core", null, "streamfilethreshold", getStreamFileThreshold()); //$NON-NLS-1$ //$NON-NLS-2$
+		long sft = rc.getLong(CONFIG_CORE_SECTION, null,
+				CONFIG_KEY_STREAM_FILE_TRESHOLD, getStreamFileThreshold());
 		sft = Math.min(sft, maxMem / 4); // don't use more than 1/4 of the heap
 		sft = Math.min(sft, Integer.MAX_VALUE); // cannot exceed array length
 		setStreamFileThreshold((int) sft);
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/storage/file/WindowCacheStats.java b/org.eclipse.jgit/src/org/eclipse/jgit/storage/file/WindowCacheStats.java
index b7f6394df6..65f8dae342 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/storage/file/WindowCacheStats.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/storage/file/WindowCacheStats.java
@@ -42,6 +42,8 @@
  */
 package org.eclipse.jgit.storage.file;
 
+import java.util.Map;
+
 import javax.management.MXBean;
 
 import org.eclipse.jgit.internal.storage.file.WindowCache;
@@ -226,6 +228,13 @@ public interface WindowCacheStats {
 	long getOpenByteCount();
 
 	/**
+	 * Number of bytes cached per repository
+	 *
+	 * @return number of bytes cached per repository
+	 */
+	Map<String, Long> getOpenByteCountPerRepository();
+
+	/**
 	 * Reset counters. Does not reset open bytes and open files counters.
 	 */
 	void resetCounters();
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/AbstractTreeIterator.java b/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/AbstractTreeIterator.java
index 335abe1b5b..a3c93cf87a 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/AbstractTreeIterator.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/AbstractTreeIterator.java
@@ -239,12 +239,10 @@ public abstract class AbstractTreeIterator {
 		path = p.path;
 		pathOffset = p.pathLen + 1;
 
-		try {
-			path[pathOffset - 1] = '/';
-		} catch (ArrayIndexOutOfBoundsException e) {
+		if (pathOffset > path.length) {
 			growPath(p.pathLen);
-			path[pathOffset - 1] = '/';
 		}
+		path[pathOffset - 1] = '/';
 	}
 
 	/**
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/CanonicalTreeParser.java b/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/CanonicalTreeParser.java
index 019968875d..b2d8fc3aa8 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/CanonicalTreeParser.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/treewalk/CanonicalTreeParser.java
@@ -387,14 +387,13 @@ public class CanonicalTreeParser extends AbstractTreeIterator {
 		tmp = pathOffset;
 		for (;; tmp++) {
 			c = raw[ptr++];
-			if (c == 0)
+			if (c == 0) {
 				break;
-			try {
-				path[tmp] = c;
-			} catch (ArrayIndexOutOfBoundsException e) {
+			}
+			if (tmp >= path.length) {
 				growPath(tmp);
-				path[tmp] = c;
 			}
+			path[tmp] = c;
 		}
 		pathLen = tmp;
 		nextPtr = ptr + OBJECT_ID_LENGTH;