diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/dfs/DfsGarbageCollectorTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/dfs/DfsGarbageCollectorTest.java
index bfa30d5b4..b5c73c2b0 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/dfs/DfsGarbageCollectorTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/dfs/DfsGarbageCollectorTest.java
@@ -19,7 +19,6 @@
 import java.util.concurrent.TimeUnit;
 
 import org.eclipse.jgit.internal.storage.dfs.DfsObjDatabase.PackSource;
-import org.eclipse.jgit.internal.storage.dfs.DfsRefDatabase;
 import org.eclipse.jgit.internal.storage.reftable.RefCursor;
 import org.eclipse.jgit.internal.storage.reftable.ReftableConfig;
 import org.eclipse.jgit.internal.storage.reftable.ReftableReader;
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/GcOrphanFilesTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/GcOrphanFilesTest.java
index 79d72c56d..e54c4ad45 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/GcOrphanFilesTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/GcOrphanFilesTest.java
@@ -57,11 +57,15 @@ public class GcOrphanFilesTest extends GcTestCase {
 
 	private final static String BITMAP_File_1 = PACK + "-1.bitmap";
 
-	private final static String IDX_File_2 = PACK + "-2.idx";
+	private static final String BITMAP_File_2 = PACK + "-2.bitmap";
+
+	private static final String IDX_File_2 = PACK + "-2.idx";
 
 	private final static String IDX_File_malformed = PACK + "-1234idx";
 
-	private final static String PACK_File_2 = PACK + "-2.pack";
+	private static final String KEEP_File_2 = PACK + "-2.keep";
+
+	private static final String PACK_File_2 = PACK + "-2.pack";
 
 	private final static String PACK_File_3 = PACK + "-3.pack";
 
@@ -105,6 +109,22 @@ public void malformedIdxNotDeleted() throws Exception {
 		assertTrue(new File(packDir, IDX_File_malformed).exists());
 	}
 
+	@Test
+	public void keepPreventsDeletionOfIndexFilesForMissingPackFile()
+			throws Exception {
+		createFileInPackFolder(BITMAP_File_1);
+		createFileInPackFolder(IDX_File_2);
+		createFileInPackFolder(BITMAP_File_2);
+		createFileInPackFolder(KEEP_File_2);
+		createFileInPackFolder(PACK_File_3);
+		gc.gc();
+		assertFalse(new File(packDir, BITMAP_File_1).exists());
+		assertTrue(new File(packDir, BITMAP_File_2).exists());
+		assertTrue(new File(packDir, IDX_File_2).exists());
+		assertTrue(new File(packDir, KEEP_File_2).exists());
+		assertTrue(new File(packDir, PACK_File_3).exists());
+	}
+
 	private void createFileInPackFolder(String fileName) throws IOException {
 		if (!packDir.exists() || !packDir.isDirectory()) {
 			assertTrue(packDir.mkdirs());
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/StatsTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/StatsTest.java
index 8b253828c..0303bb4f7 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/StatsTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/util/StatsTest.java
@@ -45,7 +45,6 @@
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertTrue;
 
-import org.eclipse.jgit.util.Stats;
 import org.junit.Test;
 
 public class StatsTest {
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 b734ce565..504e79389 100644
--- a/org.eclipse.jgit/resources/org/eclipse/jgit/internal/JGitText.properties
+++ b/org.eclipse.jgit/resources/org/eclipse/jgit/internal/JGitText.properties
@@ -203,6 +203,7 @@ deepenNotWithDeepen=Cannot combine deepen with deepen-not
 deepenSinceWithDeepen=Cannot combine deepen with deepen-since
 deleteBranchUnexpectedResult=Delete branch returned unexpected result {0}
 deleteFileFailed=Could not delete file {0}
+deletedOrphanInPackDir=Deleted orphaned file {}
 deleteRequiresZeroNewId=Delete requires new ID to be zero
 deleteTagUnexpectedResult=Delete tag returned unexpected result {0}
 deletingNotSupported=Deleting {0} not supported.
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/JGitText.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/JGitText.java
index f65e3746e..db3caec5c 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/JGitText.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/JGitText.java
@@ -264,6 +264,7 @@ public static JGitText get() {
 	/***/ public String deepenSinceWithDeepen;
 	/***/ public String deleteBranchUnexpectedResult;
 	/***/ public String deleteFileFailed;
+	/***/ public String deletedOrphanInPackDir;
 	/***/ public String deleteRequiresZeroNewId;
 	/***/ public String deleteTagUnexpectedResult;
 	/***/ public String deletingNotSupported;
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/GC.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/GC.java
index 791a10828..0d8d97908 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/GC.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/GC.java
@@ -148,6 +148,8 @@ public class GC {
 
 	private static final String INDEX_EXT = "." + PackExt.INDEX.getExtension(); //$NON-NLS-1$
 
+	private static final String KEEP_EXT = "." + PackExt.KEEP.getExtension(); //$NON-NLS-1$
+
 	private static final int DEFAULT_AUTOPACKLIMIT = 50;
 
 	private static final int DEFAULT_AUTOLIMIT = 6700;
@@ -978,11 +980,15 @@ private void deleteOrphans() {
 			fileNames = files.map(path -> path.getFileName().toString())
 					.filter(name -> (name.endsWith(PACK_EXT)
 							|| name.endsWith(BITMAP_EXT)
-							|| name.endsWith(INDEX_EXT)))
+							|| name.endsWith(INDEX_EXT)
+							|| name.endsWith(KEEP_EXT)))
+					// sort files with same base name in the order:
+					// .pack, .keep, .index, .bitmap to avoid look ahead
 					.sorted(Collections.reverseOrder())
 					.collect(Collectors.toList());
-		} catch (IOException e1) {
-			// ignore
+		} catch (IOException e) {
+			LOG.error(e.getMessage(), e);
+			return;
 		}
 		if (fileNames == null) {
 			return;
@@ -990,12 +996,14 @@ private void deleteOrphans() {
 
 		String base = null;
 		for (String n : fileNames) {
-			if (n.endsWith(PACK_EXT)) {
+			if (n.endsWith(PACK_EXT) || n.endsWith(KEEP_EXT)) {
 				base = n.substring(0, n.lastIndexOf('.'));
 			} else {
 				if (base == null || !n.startsWith(base)) {
 					try {
-						Files.delete(packDir.resolve(n));
+						Path delete = packDir.resolve(n);
+						Files.delete(delete);
+						LOG.warn(JGitText.get().deletedOrphanInPackDir, delete);
 					} catch (IOException e) {
 						LOG.error(e.getMessage(), e);
 					}
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/lib/GitmoduleEntry.java b/org.eclipse.jgit/src/org/eclipse/jgit/lib/GitmoduleEntry.java
index bded52751..4f2e558b2 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/lib/GitmoduleEntry.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/lib/GitmoduleEntry.java
@@ -42,8 +42,6 @@
  */
 package org.eclipse.jgit.lib;
 
-import org.eclipse.jgit.lib.AnyObjectId;
-
 /**
  * A .gitmodules file found in the pack. Store the blob of the file itself (e.g.
  * to access its contents) and the tree where it was found (e.g. to check if it