diff --git a/Tools/Java/Source/Common/build.xml b/Tools/Java/Source/Common/build.xml
index 4fd7285f01..376948c465 100644
--- a/Tools/Java/Source/Common/build.xml
+++ b/Tools/Java/Source/Common/build.xml
@@ -16,18 +16,34 @@ WITHOUT WARRANTIES OR REPRESENTATIONS OF ANY KIND, EITHER EXPRESS OR IMPLIED.
   <property name="WORKSPACE" value="${env.WORKSPACE}"/>
   <property name="buildDir" value="build"/>
   <property name="installLocation" value="${WORKSPACE}/Tools/Jars"/>
+
+  <path id="classpath">
+    <fileset dir="${WORKSPACE}/Tools/Jars">
+      <include name="SurfaceArea.jar"/>
+    </fileset>
+    <fileset dir="${env.XMLBEANS_HOME}/lib">
+      <include name="*.jar"/>
+    </fileset>
+    <pathelement path="${env.CLASSPATH}"/>
+  </path>
+
   <target name="Common_Jar" depends="install"/>
+
   <target name="source">
     <mkdir dir="${buildDir}"/>
     <javac srcdir="." destdir="${buildDir}">
+      <classpath refid="classpath"/>
       <compilerarg value="-Xlint"/>
     </javac>
   </target>
+
   <target name="clean">
-    <delete dir="${buildDir}"/>
+    <delete includeemptydirs="true" failonerror="false">
+      <fileset dir="${WORKSPACE}/Tools/Java/Source/Common" includes="${buildDir}"/>
+    </delete>
   </target>
-  <target name="cleanall">
-    <delete dir="${buildDir}"/>
+
+  <target name="cleanall" depends="clean">
     <delete file="${installLocation}/Common.jar"/>
     <if>
       <available file="${installLocation}/Common.jar"/>
@@ -37,6 +53,7 @@ WITHOUT WARRANTIES OR REPRESENTATIONS OF ANY KIND, EITHER EXPRESS OR IMPLIED.
       </then>
     </if>
   </target>
+
   <target name="install" depends="source">
     <jar destfile="${installLocation}/Common.jar"
       basedir="${buildDir}"
diff --git a/Tools/Java/Source/ContextTool/build.xml b/Tools/Java/Source/ContextTool/build.xml
index 13567799b4..65f75456f7 100644
--- a/Tools/Java/Source/ContextTool/build.xml
+++ b/Tools/Java/Source/ContextTool/build.xml
@@ -30,10 +30,11 @@ WITHOUT WARRANTIES OR REPRESENTATIONS OF ANY KIND, EITHER EXPRESS OR IMPLIED.
     </javac>
   </target>
   <target name="clean">
-    <delete dir="${buildDir}"/>
+    <delete includeemptydirs="true" failonerror="false" quiet="true">
+      <fileset dir="${WORKSPACE}/Tools/Java/Source/ContextTool" includes="${buildDir}"/>
+    </delete>
   </target>
-  <target name="cleanall">
-    <delete dir="${buildDir}"/>
+  <target name="cleanall" depends="clean">
     <delete file="${installLocation}/ContextTool.jar"/>
     <if>
       <available file="${installLocation}/ContextTool.jar"/>
diff --git a/Tools/Java/Source/Cpptasks/build.xml b/Tools/Java/Source/Cpptasks/build.xml
index 15eb959820..971e7e774c 100644
--- a/Tools/Java/Source/Cpptasks/build.xml
+++ b/Tools/Java/Source/Cpptasks/build.xml
@@ -32,10 +32,11 @@ WITHOUT WARRANTIES OR REPRESENTATIONS OF ANY KIND, EITHER EXPRESS OR IMPLIED.
     </javac>
   </target>
   <target name="clean">
-    <delete dir="${buildDir}"/>
+    <delete includeemptydirs="true" failonerror="false">
+      <fileset dir="${WORKSPACE}/Tools/Java/Source/Cpptasks" includes="${buildDir}"/>
+    </delete>
   </target>
-  <target name="cleanall">
-    <delete dir="${buildDir}"/>
+  <target name="cleanall" depends="clean">
     <delete file="${installLocation}/cpptasks.jar"/>
     <if>
       <available file="${installLocation}/cpptasks.jar"/>
diff --git a/Tools/Java/Source/FrameworkTasks/build.xml b/Tools/Java/Source/FrameworkTasks/build.xml
index ac3639cb0c..ad5d3f0ff9 100644
--- a/Tools/Java/Source/FrameworkTasks/build.xml
+++ b/Tools/Java/Source/FrameworkTasks/build.xml
@@ -28,10 +28,11 @@ WITHOUT WARRANTIES OR REPRESENTATIONS OF ANY KIND, EITHER EXPRESS OR IMPLIED.
     </javac>
   </target>
   <target name="clean">
-    <delete dir="${buildDir}"/>
+    <delete includeemptydirs="true" failonerror="false" quiet="true">
+      <fileset dir="${WORKSPACE}/Tools/Java/Source/FrameworkTasks" includes="${buildDir}"/>
+    </delete>
   </target>
-  <target name="cleanall">
-    <delete dir="${buildDir}"/>
+  <target name="cleanall" depends="clean">
     <delete file="${installLocation}/frameworktasks.jar"/>
     <if>
       <available file="${installLocation}/frameworktasks.jar"/>
diff --git a/Tools/Java/Source/FrameworkWizard/build.xml b/Tools/Java/Source/FrameworkWizard/build.xml
index b9fc0b495b..c936930254 100644
--- a/Tools/Java/Source/FrameworkWizard/build.xml
+++ b/Tools/Java/Source/FrameworkWizard/build.xml
@@ -29,10 +29,11 @@ WITHOUT WARRANTIES OR REPRESENTATIONS OF ANY KIND, EITHER EXPRESS OR IMPLIED.
     </javac>
   </target>
   <target name="clean">
-    <delete dir="${buildDir}"/>
+    <delete includeemptydirs="true" failonerror="false" quiet="true">
+      <fileset dir="${WORKSPACE}/Tools/Java/Source/FrameworkWizard" includes="${buildDir}"/>
+    </delete>
   </target>
-  <target name="cleanall">
-    <delete dir="${buildDir}"/>
+  <target name="cleanall" depends="clean">
     <delete file="${installLocation}/FrameworkWizard.jar"/>
   </target>
   <target name="install" depends="source">
diff --git a/Tools/Java/Source/GenBuild/build.xml b/Tools/Java/Source/GenBuild/build.xml
index b61e2519c3..d33cbebde0 100644
--- a/Tools/Java/Source/GenBuild/build.xml
+++ b/Tools/Java/Source/GenBuild/build.xml
@@ -31,10 +31,11 @@ WITHOUT WARRANTIES OR REPRESENTATIONS OF ANY KIND, EITHER EXPRESS OR IMPLIED.
     </javac>
   </target>
   <target name="clean">
-    <delete dir="${buildDir}"/>
+    <delete includeemptydirs="true" failonerror="false" quiet="true">
+      <fileset dir="${WORKSPACE}/Tools/Java/Source/GenBuild" includes="${buildDir}"/>
+    </delete>
   </target>
-  <target name="cleanall">
-    <delete dir="${buildDir}"/>
+  <target name="cleanall" depends="clean">
     <delete file="${installLocation}/GenBuild.jar"/>
     <if>
       <available file="${installLocation}/GenBuild.jar"/>
diff --git a/Tools/Java/Source/Merge/build.xml b/Tools/Java/Source/Merge/build.xml
index e6e8aa6fce..8b91fad7cd 100644
--- a/Tools/Java/Source/Merge/build.xml
+++ b/Tools/Java/Source/Merge/build.xml
@@ -28,10 +28,11 @@ WITHOUT WARRANTIES OR REPRESENTATIONS OF ANY KIND, EITHER EXPRESS OR IMPLIED.
     </javac>
   </target>
   <target name="clean">
-    <delete dir="${buildDir}"/>
+    <delete includeemptydirs="true" failonerror="false" quiet="true">
+      <fileset dir="${WORKSPACE}/Tools/Java/Source/Merge" includes="${buildDir}"/>
+    </delete>
   </target>
-  <target name="cleanall">
-    <delete dir="${buildDir}"/>
+  <target name="cleanall" depends="clean">
     <delete file="${installLocation}/Merge.jar"/>
   </target>
   <target name="install" depends="source">
diff --git a/Tools/Java/Source/MigrationTools/build.xml b/Tools/Java/Source/MigrationTools/build.xml
index 2406c0350f..10ca9215c8 100644
--- a/Tools/Java/Source/MigrationTools/build.xml
+++ b/Tools/Java/Source/MigrationTools/build.xml
@@ -29,10 +29,11 @@ WITHOUT WARRANTIES OR REPRESENTATIONS OF ANY KIND, EITHER EXPRESS OR IMPLIED.
     </javac>
   </target>
   <target name="clean">
-    <delete dir="${buildDir}"/>
+    <delete includeemptydirs="true" failonerror="false" quiet="true">
+      <fileset dir="${WORKSPACE}/Tools/Java/Source/MigrationTools" includes="${buildDir}"/>
+    </delete>
   </target>
-  <target name="cleanall">
-    <delete dir="${buildDir}"/>
+  <target name="cleanall" depends="clean">
     <delete file="${installLocation}/MigrationTools.jar"/>
     <if>
       <available file="${installLocation}/MigrationTools.jar"/>
diff --git a/Tools/Java/Source/PcdTools/build.xml b/Tools/Java/Source/PcdTools/build.xml
index c47032e9f5..a8c7aa959f 100644
--- a/Tools/Java/Source/PcdTools/build.xml
+++ b/Tools/Java/Source/PcdTools/build.xml
@@ -30,10 +30,11 @@ WITHOUT WARRANTIES OR REPRESENTATIONS OF ANY KIND, EITHER EXPRESS OR IMPLIED.
     </javac>
   </target>
   <target name="clean">
-    <delete dir="${buildDir}"/>
+    <delete includeemptydirs="true" failonerror="false" quiet="true">
+    <fileset dir="${WORKSPACE}/Tools/Java/Source/PcdTools" includes="${buildDir}"/>
+    </delete>
   </target>
-  <target name="cleanall">
-    <delete dir="${buildDir}"/>
+  <target name="cleanall" depends="clean">
     <delete file="${installLocation}/PcdTools.jar"/>
     <if>
       <available file="${installLocation}/PcdTools.jar"/>
diff --git a/Tools/Java/Source/SurfaceArea/build.xml b/Tools/Java/Source/SurfaceArea/build.xml
index 5b0efdb625..6931d81706 100644
--- a/Tools/Java/Source/SurfaceArea/build.xml
+++ b/Tools/Java/Source/SurfaceArea/build.xml
@@ -83,7 +83,7 @@ WITHOUT WARRANTIES OR REPRESENTATIONS OF ANY KIND, EITHER EXPRESS OR IMPLIED.
   
   <target name="SurfaceArea.java.clean">
     <delete includeemptydirs="true" failonerror="false">
-      <fileset dir="${WORKSPACE}/Tools/Java/Source/SurfaceArea/org" includes="**/*"/>
+      <fileset dir="${WORKSPACE}/Tools/Java/Source/SurfaceArea" includes="org"/>
     </delete>
   </target>