diff --git a/java.source/apichanges.xml b/java.source/apichanges.xml
--- a/java.source/apichanges.xml
+++ b/java.source/apichanges.xml
@@ -105,6 +105,19 @@
     <!-- ACTUAL CHANGES BEGIN HERE: -->
 
     <changes>
+        <change id="JavaSource.patchedPublic">
+             <api name="general"/>
+             <summary>Removing the binary compatibility methods (using bytecode patching) from JavaSource</summary>
+             <version major="0" minor="46"/>
+             <date day="6" month="8" year="2009"/>
+             <author login="tzezula"/>
+             <compatibility binary="incompatible" deletion="yes" source="compatible"/>
+             <description>
+                 The JavaSource class contains methods introduced to keep binary compatibility among milestones of NB 6.0.
+                 These methods are not needed anymore and will be removed.
+             </description>
+             <class package="org.netbeans.api.java.source" name="JavaSource"/>
+        </change>
         <change id="TreeMaker.Method">
              <api name="general"/>
              <summary>Added new Method allowing creating varargs methods.</summary>
diff --git a/java.source/nbproject/project.properties b/java.source/nbproject/project.properties
--- a/java.source/nbproject/project.properties
+++ b/java.source/nbproject/project.properties
@@ -43,7 +43,7 @@
 javadoc.title=Java Source
 javadoc.arch=${basedir}/arch.xml
 javadoc.apichanges=${basedir}/apichanges.xml
-spec.version.base=0.45.0
+spec.version.base=0.46.0
 test.qa-functional.cp.extra=${refactoring.java.dir}/modules/ext/javac-api-nb-7.0-b07.jar
 test.unit.run.cp.extra=${o.n.core.dir}/core/core.jar:\
     ${o.n.core.dir}/lib/boot.jar:\
diff --git a/java.source/src/org/netbeans/api/java/source/JavaSource.java b/java.source/src/org/netbeans/api/java/source/JavaSource.java
--- a/java.source/src/org/netbeans/api/java/source/JavaSource.java
+++ b/java.source/src/org/netbeans/api/java/source/JavaSource.java
@@ -534,11 +534,6 @@
         }
     }
 
-    @PatchedPublic
-    private void runUserActionTask( final CancellableTask<CompilationController> task, final boolean shared) throws IOException {
-        final Task<CompilationController> _task = task;
-        this.runUserActionTask (_task, shared);
-    }
     
     
     long createTaggedController (final long timestamp, final Object[] controller) throws IOException {
@@ -626,11 +621,6 @@
         }
     }
 
-    @PatchedPublic
-    private Future<Void> runWhenScanFinished (final CancellableTask<CompilationController> task, final boolean shared) throws IOException {
-        final Task<CompilationController> _task = task;
-        return this.runWhenScanFinished (_task, shared);
-    }
        
     /** Runs a task which permits for modifying the sources.
      * Call to this method will cancel processing of all the phase completion tasks until
@@ -704,11 +694,6 @@
         }        
     }
 
-    @PatchedPublic
-    private ModificationResult runModificationTask(CancellableTask<WorkingCopy> task) throws IOException { 
-        final Task<WorkingCopy> _task = task;
-        return this.runModificationTask (_task);
-    }
     /**
      * Returns the classpaths ({@link ClasspathInfo}) used by this
      * {@link JavaSource}