Justify API-breaking changes introduced in 4cd9548

Use .api_filters to suppress API baseline errors. The justification is
included in comments in that file.

Change-Id: I7b5c69d8d13733719b28ef7317fc9780ed2828d8
Signed-off-by: Matthew DeVore <matvore@gmail.com>

org.eclipse.jgit/.settings/.api_filters

@@ -1,5 +1,28 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <component id="org.eclipse.jgit" version="2">
+    <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 comment="API was only non-final for one version, so unlikely to be overridden" id="1141899266">
+            <message_arguments>
+                <message_argument value="5.3"/>
+                <message_argument value="5.4"/>
+                <message_argument value="getFilterBlobLimit()"/>
+            </message_arguments>
+        </filter>
+    </resource>
     <resource path="src/org/eclipse/jgit/util/FS.java" type="org.eclipse.jgit.util.FS">
         <filter id="1142947843">
             <message_arguments>