diff --git a/org.eclipse.jgit.lfs.server/.settings/.api_filters b/org.eclipse.jgit.lfs.server/.settings/.api_filters
index 3e60680cf..6609c3d40 100644
--- a/org.eclipse.jgit.lfs.server/.settings/.api_filters
+++ b/org.eclipse.jgit.lfs.server/.settings/.api_filters
@@ -1,13 +1,5 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <component id="org.eclipse.jgit.lfs.server" version="2">
-    <resource path="META-INF/MANIFEST.MF">
-        <filter id="924844039">
-            <message_arguments>
-                <message_argument value="5.2.3"/>
-                <message_argument value="5.2.0"/>
-            </message_arguments>
-        </filter>
-    </resource>
     <resource path="src/org/eclipse/jgit/lfs/server/fs/ObjectUploadListener.java" type="org.eclipse.jgit.lfs.server.fs.ObjectUploadListener">
         <filter id="1142947843">
             <message_arguments>
diff --git a/org.eclipse.jgit.lfs/.settings/.api_filters b/org.eclipse.jgit.lfs/.settings/.api_filters
deleted file mode 100644
index 95a45574e..000000000
--- a/org.eclipse.jgit.lfs/.settings/.api_filters
+++ /dev/null
@@ -1,11 +0,0 @@
-<?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="5.2.3"/>
-                <message_argument value="5.2.0"/>
-            </message_arguments>
-        </filter>
-    </resource>
-</component>
diff --git a/org.eclipse.jgit/.settings/.api_filters b/org.eclipse.jgit/.settings/.api_filters
index cbb9de113..857fcac17 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="5.2.3"/>
-                <message_argument value="5.2.0"/>
-            </message_arguments>
-        </filter>
-    </resource>
     <resource path="src/org/eclipse/jgit/dircache/DirCacheEntry.java" type="org.eclipse.jgit.dircache.DirCacheEntry">
         <filter id="1142947843">
             <message_arguments>
@@ -42,6 +34,28 @@
             </message_arguments>
         </filter>
     </resource>
+    <resource path="src/org/eclipse/jgit/gitrepo/RepoCommand.java" type="org.eclipse.jgit.gitrepo.RepoCommand$DefaultRemoteReader">
+        <filter id="338792546">
+            <message_arguments>
+                <message_argument value="org.eclipse.jgit.gitrepo.RepoCommand.DefaultRemoteReader"/>
+                <message_argument value="readFile(String, String, String)"/>
+            </message_arguments>
+        </filter>
+        <filter id="338792546">
+            <message_arguments>
+                <message_argument value="org.eclipse.jgit.gitrepo.RepoCommand.DefaultRemoteReader"/>
+                <message_argument value="readFileFromRepo(Repository, String, String)"/>
+            </message_arguments>
+        </filter>
+    </resource>
+    <resource path="src/org/eclipse/jgit/gitrepo/RepoCommand.java" type="org.eclipse.jgit.gitrepo.RepoCommand$RemoteReader">
+        <filter id="403804204">
+            <message_arguments>
+                <message_argument value="org.eclipse.jgit.gitrepo.RepoCommand.RemoteReader"/>
+                <message_argument value="readFileWithMode(String, String, String)"/>
+            </message_arguments>
+        </filter>
+    </resource>
     <resource path="src/org/eclipse/jgit/lib/ConfigConstants.java" type="org.eclipse.jgit.lib.ConfigConstants">
         <filter id="1142947843">
             <message_arguments>
@@ -62,6 +76,42 @@
             </message_arguments>
         </filter>
     </resource>
+    <resource path="src/org/eclipse/jgit/lib/GitmoduleEntry.java" type="org.eclipse.jgit.lib.GitmoduleEntry">
+        <filter id="1109393411">
+            <message_arguments>
+                <message_argument value="4.7.5"/>
+                <message_argument value="org.eclipse.jgit.lib.GitmoduleEntry"/>
+            </message_arguments>
+        </filter>
+    </resource>
+    <resource path="src/org/eclipse/jgit/lib/ObjectChecker.java" type="org.eclipse.jgit.lib.ObjectChecker">
+        <filter id="1142947843">
+            <message_arguments>
+                <message_argument value="4.7.5"/>
+                <message_argument value="getGitsubmodules()"/>
+            </message_arguments>
+        </filter>
+    </resource>
+    <resource path="src/org/eclipse/jgit/revwalk/DepthWalk.java" type="org.eclipse.jgit.revwalk.DepthWalk">
+        <filter id="403804204">
+            <message_arguments>
+                <message_argument value="org.eclipse.jgit.revwalk.DepthWalk"/>
+                <message_argument value="getDeepenNotFlag()"/>
+            </message_arguments>
+        </filter>
+        <filter id="404000815">
+            <message_arguments>
+                <message_argument value="org.eclipse.jgit.revwalk.DepthWalk"/>
+                <message_argument value="getDeepenNots()"/>
+            </message_arguments>
+        </filter>
+        <filter id="404000815">
+            <message_arguments>
+                <message_argument value="org.eclipse.jgit.revwalk.DepthWalk"/>
+                <message_argument value="getDeepenSince()"/>
+            </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>
@@ -118,6 +168,14 @@
             </message_arguments>
         </filter>
     </resource>
+    <resource path="src/org/eclipse/jgit/transport/RemoteSession.java" type="org.eclipse.jgit.transport.RemoteSession">
+        <filter id="404000815">
+            <message_arguments>
+                <message_argument value="org.eclipse.jgit.transport.RemoteSession"/>
+                <message_argument value="getFtpChannel()"/>
+            </message_arguments>
+        </filter>
+    </resource>
     <resource path="src/org/eclipse/jgit/transport/TransferConfig.java" type="org.eclipse.jgit.transport.TransferConfig">
         <filter id="1159725059">
             <message_arguments>
@@ -132,6 +190,14 @@
             </message_arguments>
         </filter>
     </resource>
+    <resource path="src/org/eclipse/jgit/transport/http/HttpConnection.java" type="org.eclipse.jgit.transport.http.HttpConnection">
+        <filter id="403804204">
+            <message_arguments>
+                <message_argument value="org.eclipse.jgit.transport.http.HttpConnection"/>
+                <message_argument value="getHeaderFields(String)"/>
+            </message_arguments>
+        </filter>
+    </resource>
     <resource path="src/org/eclipse/jgit/treewalk/WorkingTreeIterator.java" type="org.eclipse.jgit.treewalk.WorkingTreeIterator">
         <filter id="1142947843">
             <message_arguments>