Index: maven-assembly-plugin/src/main/java/org/apache/maven/plugin/assembly/archive/ManifestCreationFinalizer.java
===================================================================
--- maven-assembly-plugin/src/main/java/org/apache/maven/plugin/assembly/archive/ManifestCreationFinalizer.java	(revision 549497)
+++ maven-assembly-plugin/src/main/java/org/apache/maven/plugin/assembly/archive/ManifestCreationFinalizer.java	(working copy)
@@ -72,7 +72,7 @@
                 }
                 else
                 {
-                    manifest = mavenArchiver.getManifest( project, archiveConfiguration.getManifest() );
+                    manifest = mavenArchiver.getManifest( project, archiveConfiguration );
                 }
 
                 if ( manifest != null && ( archiver instanceof JarArchiver ) )
Index: maven-assembly-plugin/pom.xml
===================================================================
--- maven-assembly-plugin/pom.xml	(revision 549497)
+++ maven-assembly-plugin/pom.xml	(working copy)
@@ -249,9 +249,6 @@
               <pomExcludes>
                 <pomExclude>**/child*/pom.xml</pomExclude>
                 <pomExclude>**/module*/pom.xml</pomExclude>
-
-                <!-- TODO: Fix this! It's logged in JIRA for 2.2. -->
-                <pomExclude>mojo-configuration/manifest-with-customEntry/pom.xml</pomExclude>
                 <pomExclude>repository-assembly/pom.xml</pomExclude>
               </pomExcludes>
               <postBuildHookScript>verify.bsh</postBuildHookScript>