diff --git a/org.eclipse.jgit/.settings/.api_filters b/org.eclipse.jgit/.settings/.api_filters
new file mode 100644
index 0000000..a6aff1b
--- /dev/null
+++ b/org.eclipse.jgit/.settings/.api_filters
@@ -0,0 +1,101 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<component id="org.eclipse.jgit" version="2">
+    <resource path="src/org/eclipse/jgit/api/GarbageCollectCommand.java" type="org.eclipse.jgit.api.GarbageCollectCommand">
+        <filter id="1142947843">
+            <message_arguments>
+                <message_argument value="5.13.3"/>
+                <message_argument value="setPackKeptObjects(boolean)"/>
+            </message_arguments>
+        </filter>
+    </resource>
+    <resource path="src/org/eclipse/jgit/dircache/Checkout.java" type="org.eclipse.jgit.dircache.Checkout">
+        <filter id="1109393411">
+            <message_arguments>
+                <message_argument value="6.6.1"/>
+                <message_argument value="org.eclipse.jgit.dircache.Checkout"/>
+            </message_arguments>
+        </filter>
+    </resource>
+    <resource path="src/org/eclipse/jgit/errors/PackMismatchException.java" type="org.eclipse.jgit.errors.PackMismatchException">
+        <filter id="1142947843">
+            <message_arguments>
+                <message_argument value="5.9.1"/>
+                <message_argument value="isPermanent()"/>
+            </message_arguments>
+        </filter>
+        <filter id="1142947843">
+            <message_arguments>
+                <message_argument value="5.9.1"/>
+                <message_argument value="setPermanent(boolean)"/>
+            </message_arguments>
+        </filter>
+    </resource>
+    <resource path="src/org/eclipse/jgit/lib/ConfigConstants.java" type="org.eclipse.jgit.lib.ConfigConstants">
+        <filter id="1142947843">
+            <message_arguments>
+                <message_argument value="5.13.2"/>
+                <message_argument value="CONFIG_KEY_SKIPHASH"/>
+            </message_arguments>
+        </filter>
+        <filter id="1142947843">
+            <message_arguments>
+                <message_argument value="5.13.3"/>
+                <message_argument value="CONFIG_KEY_PACK_KEPT_OBJECTS"/>
+            </message_arguments>
+        </filter>
+        <filter id="1142947843">
+            <message_arguments>
+                <message_argument value="5.13.3"/>
+                <message_argument value="CONFIG_REPACK_SECTION"/>
+            </message_arguments>
+        </filter>
+    </resource>
+    <resource path="src/org/eclipse/jgit/lib/FileModeCache.java" type="org.eclipse.jgit.lib.FileModeCache">
+        <filter id="1109393411">
+            <message_arguments>
+                <message_argument value="6.6.1"/>
+                <message_argument value="org.eclipse.jgit.lib.FileModeCache"/>
+            </message_arguments>
+        </filter>
+    </resource>
+    <resource path="src/org/eclipse/jgit/revwalk/RevCommit.java" type="org.eclipse.jgit.revwalk.RevCommit">
+        <filter id="1193279491">
+            <message_arguments>
+                <message_argument value="6.5.1"/>
+                <message_argument value="buffer"/>
+            </message_arguments>
+        </filter>
+    </resource>
+    <resource path="src/org/eclipse/jgit/storage/pack/PackConfig.java" type="org.eclipse.jgit.storage.pack.PackConfig">
+        <filter id="336658481">
+            <message_arguments>
+                <message_argument value="org.eclipse.jgit.storage.pack.PackConfig"/>
+                <message_argument value="DEFAULT_PACK_KEPT_OBJECTS"/>
+            </message_arguments>
+        </filter>
+        <filter id="336658481">
+            <message_arguments>
+                <message_argument value="org.eclipse.jgit.storage.pack.PackConfig"/>
+                <message_argument value="DEFAULT_WRITE_REVERSE_INDEX"/>
+            </message_arguments>
+        </filter>
+        <filter id="1142947843">
+            <message_arguments>
+                <message_argument value="5.13.3"/>
+                <message_argument value="DEFAULT_PACK_KEPT_OBJECTS"/>
+            </message_arguments>
+        </filter>
+        <filter id="1142947843">
+            <message_arguments>
+                <message_argument value="5.13.3"/>
+                <message_argument value="isPackKeptObjects()"/>
+            </message_arguments>
+        </filter>
+        <filter id="1142947843">
+            <message_arguments>
+                <message_argument value="5.13.3"/>
+                <message_argument value="setPackKeptObjects(boolean)"/>
+            </message_arguments>
+        </filter>
+    </resource>
+</component>
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/RefDirectory.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/RefDirectory.java
index 912c89b..8bf6c67 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/RefDirectory.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/RefDirectory.java
@@ -800,7 +800,7 @@
 						}
 						Ref packedRef = newPacked.get(refName);
 						ObjectId clr_oid = currentLooseRef.getObjectId();
-						if (clr_oid != null
+						if (clr_oid != null && packedRef != null
 								&& clr_oid.equals(packedRef.getObjectId())) {
 							RefList<LooseRef> curLoose, newLoose;
 							do {