diff --git a/org.eclipse.jgit.lfs.server/.settings/.api_filters b/org.eclipse.jgit.lfs.server/.settings/.api_filters
deleted file mode 100644
index 6609c3d40..000000000
--- a/org.eclipse.jgit.lfs.server/.settings/.api_filters
+++ /dev/null
@@ -1,19 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<component id="org.eclipse.jgit.lfs.server" version="2">
-    <resource path="src/org/eclipse/jgit/lfs/server/fs/ObjectUploadListener.java" type="org.eclipse.jgit.lfs.server.fs.ObjectUploadListener">
-        <filter id="1142947843">
-            <message_arguments>
-                <message_argument value="5.1.7"/>
-                <message_argument value="setCallback(ObjectUploadListener.Callback)"/>
-            </message_arguments>
-        </filter>
-    </resource>
-    <resource path="src/org/eclipse/jgit/lfs/server/fs/ObjectUploadListener.java" type="org.eclipse.jgit.lfs.server.fs.ObjectUploadListener$Callback">
-        <filter id="1142947843">
-            <message_arguments>
-                <message_argument value="5.1.7"/>
-                <message_argument value="Callback"/>
-            </message_arguments>
-        </filter>
-    </resource>
-</component>
diff --git a/org.eclipse.jgit.lfs/.settings/.api_filters b/org.eclipse.jgit.lfs/.settings/.api_filters
new file mode 100644
index 000000000..5b8ece617
--- /dev/null
+++ b/org.eclipse.jgit.lfs/.settings/.api_filters
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<component id="org.eclipse.jgit.lfs" version="2">
+    <resource path="META-INF/MANIFEST.MF">
+        <filter id="924844039">
+            <message_arguments>
+                <message_argument value="5.4.1"/>
+                <message_argument value="5.4.0"/>
+            </message_arguments>
+        </filter>
+    </resource>
+</component>
diff --git a/org.eclipse.jgit/.settings/.api_filters b/org.eclipse.jgit/.settings/.api_filters
index 46a94193f..2f6d2fa1d 100644
--- a/org.eclipse.jgit/.settings/.api_filters
+++ b/org.eclipse.jgit/.settings/.api_filters
@@ -1,5 +1,13 @@
 <?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="5.4.1"/>
+                <message_argument value="5.4.0"/>
+            </message_arguments>
+        </filter>
+    </resource>
     <resource path="src/org/eclipse/jgit/dircache/DirCacheEntry.java" type="org.eclipse.jgit.dircache.DirCacheEntry">
         <filter id="1142947843">
             <message_arguments>
@@ -20,20 +28,6 @@
             </message_arguments>
         </filter>
     </resource>
-    <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="4.5.7"/>
-                <message_argument value="PackInvalidException(String, Throwable)"/>
-            </message_arguments>
-        </filter>
-    </resource>
     <resource path="src/org/eclipse/jgit/lib/ConfigConstants.java" type="org.eclipse.jgit.lib.ConfigConstants">
         <filter id="1142947843">
             <message_arguments>
@@ -54,30 +48,6 @@
             </message_arguments>
         </filter>
     </resource>
-    <resource path="src/org/eclipse/jgit/lib/Ref.java" type="org.eclipse.jgit.lib.Ref">
-        <filter id="403767336">
-            <message_arguments>
-                <message_argument value="org.eclipse.jgit.lib.Ref"/>
-                <message_argument value="UNDEFINED_UPDATE_INDEX"/>
-            </message_arguments>
-        </filter>
-    </resource>
-    <resource path="src/org/eclipse/jgit/lib/Repository.java" type="org.eclipse.jgit.lib.Repository">
-        <filter id="336695337">
-            <message_arguments>
-                <message_argument value="org.eclipse.jgit.lib.Repository"/>
-                <message_argument value="getIdentifier()"/>
-            </message_arguments>
-        </filter>
-    </resource>
-    <resource path="src/org/eclipse/jgit/revwalk/ObjectWalk.java" type="org.eclipse.jgit.revwalk.ObjectWalk">
-        <filter comment="ignore the risk subclasses could define the same field and cause a name clash" id="336658481">
-            <message_arguments>
-                <message_argument value="org.eclipse.jgit.revwalk.ObjectWalk"/>
-                <message_argument value="SIMPLE_VISITATION_POLICY"/>
-            </message_arguments>
-        </filter>
-    </resource>
     <resource path="src/org/eclipse/jgit/storage/file/FileBasedConfig.java" type="org.eclipse.jgit.storage.file.FileBasedConfig">
         <filter id="1142947843">
             <message_arguments>
@@ -86,112 +56,6 @@
             </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_MINSIZE_PREVENT_RACY_PACK"/>
-            </message_arguments>
-        </filter>
-        <filter id="336658481">
-            <message_arguments>
-                <message_argument value="org.eclipse.jgit.storage.pack.PackConfig"/>
-                <message_argument value="DEFAULT_WAIT_PREVENT_RACY_PACK"/>
-            </message_arguments>
-        </filter>
-        <filter id="1142947843">
-            <message_arguments>
-                <message_argument value="5.1.8"/>
-                <message_argument value="DEFAULT_MINSIZE_PREVENT_RACY_PACK"/>
-            </message_arguments>
-        </filter>
-        <filter id="1142947843">
-            <message_arguments>
-                <message_argument value="5.1.8"/>
-                <message_argument value="DEFAULT_WAIT_PREVENT_RACY_PACK"/>
-            </message_arguments>
-        </filter>
-        <filter id="1142947843">
-            <message_arguments>
-                <message_argument value="5.1.8"/>
-                <message_argument value="doWaitPreventRacyPack(long)"/>
-            </message_arguments>
-        </filter>
-        <filter id="1142947843">
-            <message_arguments>
-                <message_argument value="5.1.8"/>
-                <message_argument value="getMinSizePreventRacyPack()"/>
-            </message_arguments>
-        </filter>
-        <filter id="1142947843">
-            <message_arguments>
-                <message_argument value="5.1.8"/>
-                <message_argument value="isWaitPreventRacyPack()"/>
-            </message_arguments>
-        </filter>
-        <filter id="1142947843">
-            <message_arguments>
-                <message_argument value="5.1.8"/>
-                <message_argument value="setMinSizePreventRacyPack(long)"/>
-            </message_arguments>
-        </filter>
-        <filter id="1142947843">
-            <message_arguments>
-                <message_argument value="5.1.8"/>
-                <message_argument value="setWaitPreventRacyPack(boolean)"/>
-            </message_arguments>
-        </filter>
-    </resource>
-    <resource path="src/org/eclipse/jgit/storage/pack/PackStatistics.java" type="org.eclipse.jgit.storage.pack.PackStatistics$Accumulator">
-        <filter comment="ignore the risk subclasses could define the same field and cause a name clash" id="336658481">
-            <message_arguments>
-                <message_argument value="org.eclipse.jgit.storage.pack.PackStatistics.Accumulator"/>
-                <message_argument value="treesTraversed"/>
-            </message_arguments>
-        </filter>
-    </resource>
-    <resource path="src/org/eclipse/jgit/transport/HttpConfig.java" type="org.eclipse.jgit.transport.HttpConfig">
-        <filter id="336658481">
-            <message_arguments>
-                <message_argument value="org.eclipse.jgit.transport.HttpConfig"/>
-                <message_argument value="COOKIE_FILE_CACHE_LIMIT_KEY"/>
-            </message_arguments>
-        </filter>
-        <filter id="336658481">
-            <message_arguments>
-                <message_argument value="org.eclipse.jgit.transport.HttpConfig"/>
-                <message_argument value="COOKIE_FILE_KEY"/>
-            </message_arguments>
-        </filter>
-        <filter id="336658481">
-            <message_arguments>
-                <message_argument value="org.eclipse.jgit.transport.HttpConfig"/>
-                <message_argument value="SAVE_COOKIES_KEY"/>
-            </message_arguments>
-        </filter>
-    </resource>
-    <resource path="src/org/eclipse/jgit/transport/Transport.java" type="org.eclipse.jgit.transport.Transport">
-        <filter comment="Marked as final since overriding a deprecated stub is likely a mistake" id="421654647">
-            <message_arguments>
-                <message_argument value="org.eclipse.jgit.transport.Transport"/>
-                <message_argument value="getFilterBlobLimit()"/>
-            </message_arguments>
-        </filter>
-        <filter comment="Marked as final since overriding a deprecated stub is likely a mistake" id="421654647">
-            <message_arguments>
-                <message_argument value="org.eclipse.jgit.transport.Transport"/>
-                <message_argument value="setFilterBlobLimit(long)"/>
-            </message_arguments>
-        </filter>
-    </resource>
-    <resource path="src/org/eclipse/jgit/transport/UploadPack.java" type="org.eclipse.jgit.transport.UploadPack">
-        <filter id="421654647">
-            <message_arguments>
-                <message_argument value="org.eclipse.jgit.transport.UploadPack"/>
-                <message_argument value="getFilterBlobLimit()"/>
-            </message_arguments>
-        </filter>
-    </resource>
     <resource path="src/org/eclipse/jgit/treewalk/WorkingTreeIterator.java" type="org.eclipse.jgit.treewalk.WorkingTreeIterator">
         <filter id="1142947843">
             <message_arguments>
@@ -215,6 +79,12 @@
         </filter>
     </resource>
     <resource path="src/org/eclipse/jgit/util/FS.java" type="org.eclipse.jgit.util.FS">
+        <filter id="338792546">
+            <message_arguments>
+                <message_argument value="org.eclipse.jgit.util.FS"/>
+                <message_argument value="getFsTimerResolution(Path)"/>
+            </message_arguments>
+        </filter>
         <filter id="1142947843">
             <message_arguments>
                 <message_argument value="5.1.9"/>
@@ -262,34 +132,6 @@
             </message_arguments>
         </filter>
     </resource>
-    <resource path="src/org/eclipse/jgit/util/FileUtils.java" type="org.eclipse.jgit.util.FileUtils">
-        <filter id="1142947843">
-            <message_arguments>
-                <message_argument value="5.1.8"/>
-                <message_argument value="touch(Path)"/>
-            </message_arguments>
-        </filter>
-    </resource>
-    <resource path="src/org/eclipse/jgit/util/HttpSupport.java" type="org.eclipse.jgit.util.HttpSupport">
-        <filter id="336658481">
-            <message_arguments>
-                <message_argument value="org.eclipse.jgit.util.HttpSupport"/>
-                <message_argument value="HDR_COOKIE"/>
-            </message_arguments>
-        </filter>
-        <filter id="336658481">
-            <message_arguments>
-                <message_argument value="org.eclipse.jgit.util.HttpSupport"/>
-                <message_argument value="HDR_SET_COOKIE"/>
-            </message_arguments>
-        </filter>
-        <filter id="336658481">
-            <message_arguments>
-                <message_argument value="org.eclipse.jgit.util.HttpSupport"/>
-                <message_argument value="HDR_SET_COOKIE2"/>
-            </message_arguments>
-        </filter>
-    </resource>
     <resource path="src/org/eclipse/jgit/util/SimpleLruCache.java" type="org.eclipse.jgit.util.SimpleLruCache">
         <filter id="1109393411">
             <message_arguments>