diff --git a/ant/build.xml b/ant/build.xml
deleted file mode 100644
index ccb6a8ed..00000000
--- a/ant/build.xml
+++ /dev/null
@@ -1,994 +0,0 @@
-<!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-   Filename: $RCSfile$
-   Purpose:  Ant build file for EvA2.
-
-             Ant-Download: http://jakarta.apache.org/ant
-             Ant-Manual:   http://jakarta.apache.org/ant/manual/index.html
-
-   Precondition: 1. Ant should be installed.
-                 2. JAVA_HOME environment variable contains the path to JDK1.5 or higher
-                 3. ANT_HOME environment variable contains the path to ant's home directory
-
-   Language: XML
-   Compiler: Ant
-   Authors:  M.Kronfeld, H.Planatscher, Holger Ulmer, Felix Streichert, Joerg Wegner
-   Version:  $Revision: 284 $
-             $Date: 2007-11-27 14:37:05 +0100 (Tue, 27 Nov 2007) $
-             $Author: mkron $
-   Copyright (c) Dept. Computer Architecture, University of Tuebingen, Germany
-+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
-
-<project name="EvA2" default="compile" basedir="..">
-
-<!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-        Set properties
-+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
-	<!-- EvA2 PROPERTIES -->
-	
-  <!-- SET THE DIRECTORY PROPERTIES -->
-  <property name="source.directory"               value="src" />
-  <property name="ant.directory"               	  value="ant" />
-  <property name="build.directory"                value="build" />
-  <property name="distribution.directory"         value="dist" />
-  <property name="resources.directory"            value="resources" />
-  <property name="matlabinterface.basedir"        value="resources/MatlabInterface" />
-  <property name="matlabinterface.title"          value="JEInterface" />
-  <property file="${resources.directory}/EvA2.props"/>
-  
-	<property name="web.download.base"              value="/afs/cs.uni-tuebingen.de/ra/www/software/EvA2/downloads" />
-	<property name="web.download.versionprefix"			value="${web.download.base}/${EvA2Version}" />
-  <property name="doc.directory"					value="doc" />
-  <property name="htmldoc.directory.name" 			value="EvA2Doc" />
-  <property name="pdfdoc.name" 						value="EvA2Doc.pdf" />
-	<property name="source.distribution.directory"  value="${distribution.directory}/src-dist" />
-  <property name="binary.distribution.directory"  value="${distribution.directory}/bin-dist" />
-  <property name="javadoc.directory"              value="doc/api" />
-  <property name="library.directory"              value="lib" />
-  <property name="debug.flag"					  value="true" />
-	  <property name="jar.name"						value="EvA2Base" />
-	  <property name="srcpack.name"					value="EvA2BaseSrc" />
-   <!-- documentation -->
-    <property name="web.documentation.directory" 	value="/afs/cs.uni-tuebingen.de/ra/www/software/EvA2/EvA2Doc/" />
-	<property name="doc.directory" 					value="doc" />
-	<property name="htmldoc.directory.name" 		value="EvA2Doc" />
-	<property name="pdfdoc.name" 					value="EvA2Doc.pdf" />
-
-	<!-- 
-	Wanted to give a warning if a version is put online that already existed online. Ill leave it a TODO.
-	<condition property="web.currentVersionExists" else="false">
-	<available file="${web.download.base}/asdf.jar"/>
-	</condition> -->
-	
-	<!-- SET THESE PATHES IF YOU WANT TO COMPILE ADDITIONAL EvA2 PACKAGES -->
-	  <property name="JE2Probs.directory"			value="../JE2Probs" />	
-	  <property name="JE2ESModel.directory"			value="../JE2ESModel" />
-	  <property name="JE2Research.directory"		value="../JE2Research" />				
-
-	<condition property="JE2Probs.available" else="false">
-	  <available file="${JE2Probs.directory}"/>
-	</condition>
-	<condition property="JE2ESModel.available" else="false">
-	  <available file="${JE2ESModel.directory}"/>
-	</condition>
-	<condition property="JE2Research.available" else="false">
-	  <available file="${JE2Research.directory}"/>
-	</condition>
-	
-  <!-- SET THE BINARY LIBRARIES PROPERTIES -->
-  <property name="check.libraries.ant"            value="ant/check.xml" />
-  <property name="windows.libraries"              value="${library.directory}/windows" />
-  <property name="unix.libraries"                 value="${library.directory}/linux" />
-
-  <!-- SET THE JAVA BINARY LIBRARIES PROPERTIES -->
-  <property name="ant.java.version"               value="1.5" />
-
-  <!-- SET CLASSPATH -->
-  <path id="project.class.path">
-  	<pathelement location="." />
-  	<!-- shouldnt be required for EvA2
-    <pathelement location="${env.JAVA_HOME}/jre/lib/rt.jar" />
-    <pathelement location="${env.JAVA_HOME}/lib/dt.jar" />
-    <pathelement location="${env.JAVA_HOME}/lib/tools.jar" />
-    <pathelement location="./lib/jdom.jar" />
-    <pathelement location="./lib/xerces.jar" />
-    <pathelement location="./lib/crimson.jar" />
-    <pathelement location="./lib/xalan2.jar" />
-    <pathelement location="${build.directory}" />
-    <fileset dir="${library.directory}">
-      <include name="*.jar" />
-    </fileset>
-    -->
-  </path>
-
-  <!-- SET THE CVS RELEVANT PROPERTIES -->
-  <property name="cvs.ant"                        value="ant/cvs.xml" />
-  <property name="repository.directory.unix"      value="/afs/wsi/ra/Repository" />
-  <property name="cvs.destination.unix"           value="${source.directory}" />
-  <property name="repository.directory.windows"   value="X:/wsi/ra/Repository" />
-  <property name="cvs.destination.windows"        value="${source.directory}" />
-
-  <!-- ENVIRNONMENT PROPERTIES -->
-  <property environment="env"/>
-  
-<!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-        Usage
-+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
-
-  <target name="usage" unless="silent">
-    <echo>
-      Supported targets (default=compileAll):
-      -------------------------------------------------------------------------
-      check      - checks if all needed binary and source libraries are
-                   available.
-      compile    - compile all project files of the base package.
-      compileAll - compiles all project files of all packages.
-      javadoc    - build project javadoc files
-      binaryDist - will create a complete binary distribution
-      clean      - will clean up files, except the source files and the api
-                   documentation
-      run        - will start EvA2
-
-      use 'ant -projecthelp' for further Main targets
-    </echo>
-  </target>
-
-<!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-        Library check
-+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
-
-  <target name="check">
-    <ant inheritAll="true" antfile="${check.libraries.ant}" target="binary.libraries.test">
-      <property name="silent" value="true"/>
-    </ant>
-  </target>
-
-<!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-        Init
-+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
-
-  <target name="buildDirectories" unless="noDirectories">
-    <mkdir dir="${build.directory}" />
-    <mkdir dir="${distribution.directory}" />
-    <mkdir dir="${source.distribution.directory}" />
-    <mkdir dir="${binary.distribution.directory}" />
-    <mkdir dir="${javadoc.directory}" />
-  </target>
-
-  <target name="init">
-    <tstamp />
-    <antcall target="buildDirectories"></antcall>
-    <condition property="isWindows">
-      <and>
-        <os family="windows" />
-        <not>
-          <os family="unix" />
-        </not>
-      </and>
-    </condition>
-    <condition property="isUnix">
-      <and>
-        <os family="unix" />
-        <not>
-          <os family="windows" />
-        </not>
-      </and>
-    </condition>
-  </target>
-
-<!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-        Clean
-+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
-
-  <target name="clean" description="Cleans up project directories.">
-    <delete dir="${build.directory}" />
-    <delete dir="${distribution.directory}" />
-  </target>
-
-	<!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-		        Clean JE2Probs
-	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
-		<target name="cleanProbs" depends="usage, init, compileInfo" description="Compiles the Probs project." if="JE2Probs.available">
-		  	<ant inheritAll="false" antfile="${ant.directory}/build.xml" dir="${JE2Probs.directory}" target="clean">
-				<property name="silent" value="true"/>
-			</ant>
-		</target>
-		
-	<!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-		      Clean JE2ESModel
-	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
-		<target name="cleanESModel" depends="usage, init, compileInfo" description="Compiles the ESModel project." if="JE2ESModel.available">
-		  	<ant inheritAll="false" antfile="${ant.directory}/build.xml" dir="${JE2ESModel.directory}" target="clean">
-				<property name="silent" value="true"/>
-			</ant>
-		</target>
-		
-	<!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-		      Clean JE2Research
-	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
-		<target name="cleanResearch" depends="usage, init, compileInfo" description="Compiles the Research project." if="JE2Research.available">
-		 	<ant inheritAll="false" antfile="${ant.directory}/build.xml" dir="${JE2Research.directory}" target="clean">
-				<property name="silent" value="true"/>
-			</ant>
-		</target>
-	
-  <target name="cleanAll" depends="init, clean, cleanProbs, cleanESModel, cleanResearch">
-  </target>
-	
-<!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-        Update libraries
-+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
-  <target name="update.libraries">
-  </target>
-<!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-        Compile
-+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
-
-  <target name="compileAll" depends="compile, compileProbs, compileESModel, compileResearch" description="Update libraries and compile the project.">
-
-   </target>
-
-  <target name="compileInfo" unless="silent">
-    <tstamp />
-    <echo message="*** JE2Base Project ***"/>
-  	<echo message="Timestamp: ${DSTAMP}-${TSTAMP}"/>
-  	<echo message="Version: ${EvA2Version}" />
-    <echo message="ANT_HOME is set to = ${env.ANT_HOME}"/>
-    <echo message="JAVA_HOME is set to = ${env.JAVA_HOME}"/>
-    <echo message="You are using JDK version ${ant.java.version}"/>
-    <echo message=""/>
-    <echo message="use 'ant compileAll' - to compile all java sources (+ WSI)."/>
-    <echo message="use 'ant compile'    - to compile only the java sources (faster)."/>
-  	<echo message="JE2Probs available: ${JE2Probs.available}" />
-  	<echo message="JE2ESModel available: ${JE2ESModel.available}" />
- 	<echo message="JE2Research available: ${JE2Research.available}" />
-  </target>
-
-  <target name="compile" depends="usage, init, check, compileInfo" description="Compiles the project." >
-  <!-- COMPILE PROJECT -->
-  <javac destdir="${build.directory}" optimize="on" deprecation="on" nowarn="on" debug="${debug.flag}" >
-     <src path="${source.directory}" />
-     <exclude name="ant/**" />
-     <exclude name="build/**" />
-     <exclude name="dist/**" />
-     <exclude name="doc/**" />
-     <exclude name="resources/**" />
-     <exclude name="images/**" />
-     <exclude name="project/**" />
-	<classpath>
-        <pathelement path="${project.class.path}" />
-   <!--     <pathelement path="${library.WSI}" />
-        <pathelement path="${library.JavaNNS}" /> -->
-	<fileset dir="${library.directory}">
-        	<include name="*.jar" />
-        </fileset>
-      </classpath>
-   </javac>
-
-   <!-- GENERATE RMI STUB FILES -->
-   <rmic includes="eva2/tools/jproxy/RMIInvocationHandlerImpl.class"       stubversion="-v1.2" base="${build.directory}"/>
-   <rmic includes="eva2/tools/jproxy/RMIThreadInvocationHandlerImpl.class" stubversion="-v1.2" base="${build.directory}"/>
-
-   <!-- COPY DATA FILES TO BUILD DIRECTORY -->
-    <copy todir="${build.directory}/resources">
-      <fileset dir="${resources.directory}" includes="**/*">
-        <exclude name="**/*.xcf" />
-      </fileset>
-   </copy>
-
-  	<!-- 
-  	<copy todir="${JE2Probs.directory}/${build.directory}/resources">
-      <fileset dir="${JE2Probs.directory}/${resources.directory}" includes="**/*" />
-   </copy>
-  	
-    <copy todir="${JE2ESModel.directory}/${build.directory}/resources">
-      <fileset dir="${JE2ESModel.directory}/${resources.directory}" includes="**/*" />
-   </copy>
-    <copy todir="${JE2Research.directory}/${build.directory}/resources">
-      <fileset dir="${JE2Research.directory}/${resources.directory}" includes="**/*" />
-   </copy>  
-   -->
-  </target>
-	
-<!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-	        Compile JE2Probs
-+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
-	<target name="compileProbs" depends="usage, init, compileInfo" description="Compiles the Probs project." if="JE2Probs.available">
-	  	<ant inheritAll="false" antfile="${ant.directory}/build.xml" dir="${JE2Probs.directory}" target="compile">
-			<property name="silent" value="true"/>
-		</ant>
-	</target>
-	
-<!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-	        Dist JE2Probs
-+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
-	<target name="distProbs" depends="compileProbs" description="Build dist. of the Probs project." if="JE2Probs.available">
-	  	<ant inheritAll="false" antfile="${ant.directory}/build.xml" dir="${JE2Probs.directory}" target="dist">
-			<property name="silent" value="true"/>
-		</ant>
-	</target>
-	
-<!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-	      Compile JE2ESModel
-+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
-	<target name="compileESModel" depends="usage, init, compileInfo" description="Compiles the ESModel project." if="JE2ESModel.available">
-	  	<ant inheritAll="false" antfile="${ant.directory}/build.xml" dir="${JE2ESModel.directory}" target="compile">
-			<property name="silent" value="false"/>
-		</ant>
-	</target>
-
-<!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-	        Dist JE2ESModel
-+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
-	<target name="distESModel" depends="compileESModel" description="Build dist. of the ESModel project." if="JE2Probs.available">
-	  	<ant inheritAll="false" antfile="${ant.directory}/build.xml" dir="${JE2ESModel.directory}" target="dist">
-			<property name="silent" value="true"/>
-		</ant>
-	</target>
-	
-<!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-	      Compile JE2Research
-+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
-	<target name="compileResearch" depends="usage, init, compileInfo" description="Compiles the Research project." if="JE2Research.available">
-	 	<ant inheritAll="false" antfile="${ant.directory}/build.xml" dir="${JE2Research.directory}" target="compile">
-			<property name="silent" value="false"/>
-		</ant>
-	</target>
-		
-<!-- =================================================================== -->
-<!-- Jars all classes into one jar file                                  -->
-<!-- =================================================================== -->
-<target name="bundle" depends="compile" description="Compiles the project and puts the whole stuff into a jar-file..">
-   <property name="bin.dist.dir"  value="${binary.distribution.directory}/eva2-${DSTAMP}" />
-    <mkdir dir="${bin.dist.dir}" />
-    <mkdir dir="${bin.dist.dir}/${library.directory}" />
-<delete> <fileset dir="${bin.dist.dir}/${library.directory}" includes="*EvA*jar" /> </delete>
-<jar jarfile="${bin.dist.dir}/${library.directory}/EvA2Base.jar"  basedir="${build.directory}">
-
-<!--<fileset dir="${classes.dir}" excludes="*test*"/>-->
-<manifest> <attribute name="Main-Class" value="eva2.gui.Main"/> </manifest>
-</jar>
-</target>
-
- <!--  ===================================================================
-  -->
- <!--  Jars all classes into one jar file
-  -->
- <!--  ===================================================================
-  -->
- <target name="bundlehannes" depends="compile" description="Compiles the project and puts the whole stuff into a jar-file..">
-  <property name="bin.dist.dir" value="${binary.distribution.directory}/eva2-${DSTAMP}" />
-  <mkdir dir="${bin.dist.dir}" />
-  <mkdir dir="${bin.dist.dir}/${library.directory}" />
- <delete>
-  <fileset dir="${bin.dist.dir}/${library.directory}" includes="*EvA*jar" />
-  </delete>
- <jar jarfile="${bin.dist.dir}/${library.directory}/EvA2Base.jar" basedir="${build.directory}" filesetmanifest="mergewithoutmain">
- <!--  JKW: That's bad practice, if we have internal dependencies -->
- <!--  JKW: Use a correct shell script or ant task to run application, which  -->
- <!--  JKW: resolves the classpath automatically from all libraries in the library directory  -->
- <zipgroupfileset dir="${library.directory}">
-  <include name="**/*.jar" />
-  </zipgroupfileset>
- <!-- <fileset dir="${classes.dir}" excludes="*test*"/>
-  -->
- <manifest>
-  <attribute name="Main-Class" value="eva2.gui.Main" />
-  </manifest>
-  </jar>
-  </target>
-
-<!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-        Binary Distribution
-+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
-<target name="binaryDist" depends="compile, JEInterface" description="Compiles the project and puts the whole stuff into a jar-file..">
-    <property name="bin.dist.dir"  value="${binary.distribution.directory}/eva-${DSTAMP}" />
-    <mkdir dir="${bin.dist.dir}" />
-	<delete>
-      <fileset dir="${bin.dist.dir}/" includes="${jar.name}.jar" />
-	</delete>
-
-	<jar jarfile="${bin.dist.dir}/${jar.name}.jar"  basedir="${build.directory}" >
-	  <manifest> 
-	  	<attribute name="Main-Class" value="eva2.gui.Main"/>
-		<attribute name="Built-By" value="Center for Bioinformatics Tuebingen (ZBIT)"/>
-	  	<!--
-	  	<attribute name="Xdock:name" value="EvA2"/>
-	  	<attribute name="Xdock:icon" value="resources/images/icon4.gif"/>-->
-	  </manifest>
-	</jar>
-	
-    <copy todir="${distribution.directory}">
-      <fileset dir="${bin.dist.dir}">
-        <include name="${jar.name}.jar" />
-      </fileset>
-    </copy>
-	
-	<!--
-    <copy todir="${bin.dist.dir}/${library.directory}">
-      <fileset dir="${library.directory}">
-        <include name="**/**" />
-        <exclude name="CVS" />
-      </fileset>
-    </copy>
-
-    <copy todir="${bin.dist.dir}/ant">
-      <fileset dir="ant">
-        <include name="**/**" />
-        <exclude name="CVS" />
-      </fileset>
-    </copy>
-
-    <copy todir="${bin.dist.dir}">
-      <fileset dir=".">
-        <include name="run.sh"/>
-        <include name="run.bat"/>
-        <include name="run_eva.sh"/>
-        <include name="run_eva.bat"/>
-        <include name="*.txt"/>
-        <include name="*.html"/>
-      </fileset>
-    </copy>
-
-    <copy todir="${bin.dist.dir}/html/manual">
-      <fileset dir="html/manual">
-        <include name="**/**.gif" />
-        <include name="**/**.jpg" />
-        <include name="**/**.ps" />
-        <include name="**/**.pdf" />
-        <include name="**/**.htm" />
-        <include name="**/**.html" />
-        <exclude name="CVS, *.tar*, *.zip" />
-      </fileset>
-    </copy>
-    <copy todir="${bin.dist.dir}/${javadoc.directory}">
-      <fileset dir="${javadoc.directory}">
-        <include name="**/**" />
-      </fileset>
-    </copy>
-
-    <copy todir="${bin.dist.dir}/${tutorial.directory}">
-      <fileset dir="tutorial">
-        <include name="**/**" />
-        <exclude name="CVS" />
-      </fileset>
-    </copy>
-
-    <tar tarfile="${distribution.directory}/eva2-bin-${DSTAMP}.tar">
-      <tarfileset dir="${bin.dist.dir}">
-        <include name="**" />
-        <exclude name="*.tar*, *.zip" />
-      </tarfileset>
-    </tar>
-    <gzip zipfile="${distribution.directory}/eva2-bin-${DSTAMP}.tar.gz"
-        src="${distribution.directory}/eva2-bin-${DSTAMP}.tar" />
-    <delete file="${distribution.directory}/eva2-bin-${DSTAMP}.tar" />
-
-    <zip zipfile="${distribution.directory}/eva2-bin-${DSTAMP}.zip">
-      <zipfileset dir="${bin.dist.dir}">
-        <include name="**" />
-        <exclude name="*.tar*, *.zip" />
-      </zipfileset>
-    </zip>-->
-  </target>
-
-<!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-        Source Distribution
-+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
-
-  <target name="sourceDist" depends="init">
-  	<!--<fail message="Not properly supported yet!"/>-->
-
-    <property name="src.dist.dir"  value="${source.distribution.directory}/eva2-${DSTAMP}" />
-    <mkdir dir="${src.dist.dir}" />
-
-  	<!--<copy todir="${src.dist.dir}">
-      <fileset dir=".">
-        <include name="build.xml" />
-        <include name="build.sh" />
-        <include name="build.bat" />
-        <include name="run.sh" />
-        <include name="run.bat" />
-        <include name="*.txt" />
-      </fileset>
-    </copy>-->
-
-    <copy todir="${src.dist.dir}/${source.directory}">
-      <fileset dir="${source.directory}">
-      	<include name="**/*java" />
-      	<include name="**/*txt" />
-      </fileset>
-    </copy>
-
-    <copy todir="${src.dist.dir}/${resources.directory}">
-      <fileset dir="${resources.directory}">
-      	<include name="**/**" />
-      </fileset>
-    </copy>
-  	
-  	<copy todir="${src.dist.dir}/${ant.directory}">
-  	  <fileset dir="${ant.directory}">
-  	  	<include name="miniBuild.xml" />
-  	  </fileset>
-  	</copy>
-    
-  	<!-- rename the mini build -->
-  	<move file="${src.dist.dir}/${ant.directory}/miniBuild.xml" tofile="${src.dist.dir}/${ant.directory}/build.xml"/>
-  	
-    <mkdir dir="${src.dist.dir}/${library.directory}" />
-    <copy todir="${src.dist.dir}/${library.directory}">
-      <fileset dir="${library.directory}" includes="**jar" />
-    </copy>
-
-  	<!--<copy todir="${src.dist.dir}/doc">
-      <fileset dir="doc">
-      	<include name="**.pdf" />
-      	<include name="**.tex" />
-        <include name="**.sh" />
-        <include name="**.eps" />
-        <include name="**.gif" />
-        <include name="**.jpg" />
-        <include name="**.bib" />
-        <include name="**.bst" />
-        <include name="**.zip" />
-        <include name="**.htm" />
-        <include name="**.html" />
-      </fileset>
-    </copy>-->
-
-    <tar tarfile="${distribution.directory}/${srcpack.name}.tar"
-         basedir="${src.dist.dir}" includes="**" excludes="*.tar*, *.zip"/>
-    <gzip zipfile="${distribution.directory}/${srcpack.name}.tar.gz"
-          src="${distribution.directory}/${srcpack.name}.tar" />
-    <delete file="${distribution.directory}/${srcpack.name}.tar" />
-
-    <zip zipfile="${distribution.directory}/${srcpack.name}.zip">
-      <zipfileset dir="${src.dist.dir}">
-        <include name="**" />
-        <exclude name="*.tar*, *.zip" />
-      </zipfileset>
-    </zip>
-  </target>
-
-<!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-        Generate Distribution
-+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
-
-  <target name="dist" depends="distESModel, distProbs, binaryDist, sourceDist">
-  </target>
-	
-	<!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-	        Matlab Interface tar
-	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
-
-  <target name="JEInterface">
-    <tar tarfile="${matlabinterface.basedir}/${matlabinterface.title}.tar"
-         basedir="${matlabinterface.basedir}" includes="**" excludes="*.tar*, *.zip"/>
-  	
-    <gzip zipfile="${matlabinterface.basedir}/${matlabinterface.title}.tar.gz"
-          src="${matlabinterface.basedir}/${matlabinterface.title}.tar" />
-    <copy todir="${distribution.directory}">
-  	  <fileset dir="${matlabinterface.basedir}">
-  		<include name="${matlabinterface.title}.tar.gz" />
-  	  </fileset>
-  	</copy>
-  	<delete file="${matlabinterface.basedir}/${matlabinterface.title}.tar" />
-  	<delete file="${matlabinterface.basedir}/${matlabinterface.title}.tar.gz" />
-  	  	  	
-  </target>
-	
-<!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-	        Perform tex-to-HTML of the short documentation. Export tex from lyx manually beforehand!!!
-+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
-	<target name="docLatexToHTML" depends="init">
-		<exec dir="${doc.directory}" executable="./tex2html" os="Linux">
-		</exec>
-	</target>
-		
-<!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-	        Copy documentation to web directory. 
-	        WARNING: Note that the latex file must be brought up to date manually and that the doc is not copied to the versioned directory here.
-+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
-	<target name="docToWWW" depends="init, docLatexToHTML">
-	  	<delete>
-			<fileset dir="${web.documentation.directory}">
-				<include name="**" />
-			</fileset>
-		</delete> 
-		
-		<copy todir="${web.documentation.directory}">
-		  <fileset dir="${doc.directory}">
-			<include name="${pdfdoc.name}" />
-		  </fileset>
-		</copy>
-		<copy todir="${web.documentation.directory}">
-			<fileset dir="${doc.directory}/${htmldoc.directory.name}">
-		  		<include name="**" />
-			</fileset>
-		</copy>
-	</target>
-			
-	<!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-		        Copy www distributed version to backup directory.
-	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
-	<!-- 
-	should not be necessary any more: each revision gets its own directory
-	<target name="backupWWW" depends="initialize">
-		<mkdir dir="${web.download.base}/old-${DSTAMP}-${TSTAMP}" />
-		<copy todir="${web.download.base}/old-${DSTAMP}-${TSTAMP}">
-	      <fileset dir="${web.download.versioned}">
-	      	<include name="**Src.tar.gz" />
-	      	<include name="**.jar" />
-	      	<include name="${matlabinterface.title}.tar.gz" />
-	      </fileset>
-		  <fileset dir="${web.documentation.directory}">
-	      	<include name="**" />
-	      </fileset>
-	    </copy>		
-	</target> -->
-	
-	<!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-		        Generate Distribution and put it online. This also replaces the 
-		        Probs and ESModel packages, so keep them synchronized.
-	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
-	<target name="distToWWW" depends="init, dist, docToWWW">
-	      <fileset id="EvA2Stuff" dir="${distribution.directory}">
-	      	<include name="**Src.tar.gz" />
-	      	<include name="**.jar" />
-	      	<include name="${matlabinterface.title}.tar.gz" />
-	      </fileset>
-	      <fileset id="EvAInfo" dir="${source.directory}/eva2">
-	      	<include name="EvAInfo.java" />
-	      </fileset>
-		
-		<!-- force copy to base directory -->
-	    <copy todir="${web.download.base}" overwrite="true">
-	    	<fileset refid="EvA2Stuff"/>
-	    	<fileset refid="EvAInfo"/>
-	    </copy>
-		 <!-- copy to versioned directory -->
-	    <mkdir dir="${web.download.versionprefix}-${DSTAMP}"/>
-	    <copy todir="${web.download.versionprefix}-${DSTAMP}">
-	    	<fileset refid="EvA2Stuff"/>
-	    </copy>
-		<!-- copy doc to versioned directory -->
-		<mkdir dir="${web.download.versionprefix}-${DSTAMP}/${doc.directory}"/>
-		<copy todir="${web.download.versionprefix}-${DSTAMP}/${doc.directory}">
-			<fileset dir="${web.documentation.directory}"/>
-		</copy>
-	</target>
-	
-<!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-        Run EvA2
-+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
-
-  <target name="run" description="Runs EvA2.">
-    <java classname="eva2.gui.Main" fork="yes">
-      <jvmarg value="-Xmx512m"/>
-      <classpath>
-      	<pathelement path="${project.class.path}" />
-      	<pathelement path="${build.directory}" />
-      	</classpath>
-    </java>
-  </target>
-
-  <!--<target name="Portfolio" description="Runs GOPortfolio.">
-    <java classname="eva2.server.oa.go.GOPortfolio" fork="yes">
-        <jvmarg value="-Xmx512m" />
-        <classpath refid="project.class.path" />
-    </java>
-  </target>-->
-
-<!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-        Javadoc
-+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
-
-  <target name="javadoc" description="Generates the JavaDoc-API Documentation.">
-    <javadoc packagenames="eva2.*"
-    windowtitle ="EvA2 API Documentation"
-    doctitle    ="EvA2 API Documentation"
-    author      ="true"
-    version     ="true"
-    use         ="true"
-    destdir="${javadoc.directory}"
-    private     ="true">
-            <classpath refid="project.class.path" />
-            <sourcepath>
-              <pathelement path="${source.directory}" />
-            </sourcepath>
-            <doctitle><![CDATA[<h1>Test</h1>]]></doctitle>
-
-            <header><![CDATA[<font size="-1"><b><i>
-                             <A HREF="http://www.ra.cs.uni-tuebingen.de/software/EvA2/index.html"
-                                target="_top">EvA2
-                             </A>
-                             </b></i></font>]]>
-            </header>
-
-        <footer><![CDATA[eva2<br>
-                         <A HREF="http://www.ra.cs.uni-tuebingen.de/software/EvA2/index.html"
-                            target="_top">EvA2
-                         </A>]]>
-        </footer>
-            <link offline="true"
-                  href="http://java.sun.com/j2se/jdk1.5.0_03/docs/api/"
-                  packagelistLoc="${env.JAVA_HOME}/docs/api"
-            />
-            <link href="http://developer.java.sun.com/developer/products/xml/docs/api/"/>
-    </javadoc>
-  </target>
-
-<!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-        What's about the software design ?!;-)
-        Download required libraries from the JOELib download site:
-        http://sourceforge.net/projects/joelib
-        Package name: optional-softwaredesign-libs
-+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
-
-  <target name="pmd" depends="init" description="SOFTWAREDESIGN: Project Mess Detector !;-)">
-      <echo>Checking Project Mess Detection (PMD) rulesets.</echo>
-      <taskdef name="pmd" classname="net.sourceforge.pmd.ant.PMDTask">
-        <classpath>
-          <pathelement path="${project.class.path}" />
-          <fileset dir="${library.directory}">
-            <include name="*.jar" />
-          </fileset>
-        </classpath>
-      </taskdef>
-
-      <pmd shortFilenames="true" rulesetfiles="rulesets/basic.xml" failonerror="no">
-          <formatter type="summaryhtml" toFile="${build.directory}/pmdReport4EvA2-${DSTAMP}_basic.html"/>
-          <fileset dir="${source.directory}">
-              <include name="**/*.java"/>
-          </fileset>
-      </pmd>
-     <echo>result written to ${basedir}/${build.directory}/pmdReport4EvA2-${DSTAMP}_basic.html</echo>
-
-      <pmd shortFilenames="true" rulesetfiles="rulesets/braces.xml" failonerror="no">
-          <formatter type="summaryhtml" toFile="${build.directory}/pmdReport4EvA2-${DSTAMP}_braces.html"/>
-          <fileset dir="${source.directory}">
-              <include name="**/*.java"/>
-          </fileset>
-      </pmd>
-     <echo>result written to ${basedir}/${build.directory}/pmdReport4EvA2-${DSTAMP}_braces.html</echo>
-
-      <pmd shortFilenames="true" rulesetfiles="rulesets/codesize.xml" failonerror="no">
-          <formatter type="summaryhtml" toFile="${build.directory}/pmdReport4EvA2-${DSTAMP}_codesize.html"/>
-          <fileset dir="${source.directory}">
-              <include name="**/*.java"/>
-          </fileset>
-      </pmd>
-     <echo>result written to ${basedir}/${build.directory}/pmdReport4EvA2-${DSTAMP}_codesize.html</echo>
-
-      <pmd shortFilenames="true" rulesetfiles="rulesets/controversial.xml" failonerror="no">
-          <formatter type="summaryhtml" toFile="${build.directory}/pmdReport4EvA2-${DSTAMP}_controversial.html"/>
-          <fileset dir="${source.directory}">
-              <include name="**/*.java"/>
-          </fileset>
-      </pmd>
-     <echo>result written to ${basedir}/${build.directory}/pmdReport4EvA2-${DSTAMP}_controversial.html</echo>
-
-      <pmd shortFilenames="true" rulesetfiles="rulesets/coupling.xml" failonerror="no">
-          <formatter type="summaryhtml" toFile="${build.directory}/pmdReport4EvA2-${DSTAMP}_coupling.html"/>
-          <fileset dir="${source.directory}">
-              <include name="**/*.java"/>
-          </fileset>
-      </pmd>
-     <echo>result written to ${basedir}/${build.directory}/pmdReport4EvA2-${DSTAMP}_coupling.html</echo>
-
-      <pmd shortFilenames="true" rulesetfiles="rulesets/finalizers.xml" failonerror="no">
-          <formatter type="summaryhtml" toFile="${build.directory}/pmdReport4EvA2-${DSTAMP}_finalizers.html"/>
-          <fileset dir="${source.directory}">
-              <include name="**/*.java"/>
-          </fileset>
-      </pmd>
-     <echo>result written to ${basedir}/${build.directory}/pmdReport4EvA2-${DSTAMP}_finalizers.html</echo>
-
-      <pmd shortFilenames="true" rulesetfiles="rulesets/imports.xml" failonerror="no">
-          <formatter type="summaryhtml" toFile="${build.directory}/pmdReport4EvA2-${DSTAMP}_imports.html"/>
-          <fileset dir="${source.directory}">
-              <include name="**/*.java"/>
-          </fileset>
-      </pmd>
-     <echo>result written to ${basedir}/${build.directory}/pmdReport4EvA2-${DSTAMP}_imports.html</echo>
-
-      <pmd shortFilenames="true" rulesetfiles="rulesets/naming.xml" failonerror="no">
-          <formatter type="summaryhtml" toFile="${build.directory}/pmdReport4EvA2-${DSTAMP}_naming.html"/>
-          <fileset dir="${source.directory}">
-              <include name="**/*.java"/>
-          </fileset>
-      </pmd>
-     <echo>result written to ${basedir}/${build.directory}/pmdReport4EvA2-${DSTAMP}_naming.html</echo>
-
-      <pmd shortFilenames="true" rulesetfiles="rulesets/strictexception.xml" failonerror="no">
-          <formatter type="summaryhtml" toFile="${build.directory}/pmdReport4EvA2-${DSTAMP}_strictexception.html"/>
-          <fileset dir="${source.directory}">
-              <include name="**/*.java"/>
-          </fileset>
-      </pmd>
-     <echo>result written to ${basedir}/${build.directory}/pmdReport4EvA2-${DSTAMP}_strictexception.html</echo>
-
-      <pmd shortFilenames="true" rulesetfiles="rulesets/strings.xml" failonerror="no">
-          <formatter type="summaryhtml" toFile="${build.directory}/pmdReport4EvA2-${DSTAMP}_strings.html"/>
-          <fileset dir="${source.directory}">
-              <include name="**/*.java"/>
-          </fileset>
-      </pmd>
-     <echo>result written to ${basedir}/${build.directory}/pmdReport4EvA2-${DSTAMP}_strings.html</echo>
-
-      <pmd shortFilenames="true" rulesetfiles="rulesets/unusedcode.xml" failonerror="no">
-          <formatter type="summaryhtml" toFile="${build.directory}/pmdReport4EvA2-${DSTAMP}_unusedcode.html"/>
-          <fileset dir="${source.directory}">
-              <include name="**/*.java"/>
-          </fileset>
-      </pmd>
-     <echo>result written to ${basedir}/${build.directory}/pmdReport4EvA2-${DSTAMP}_unusedcode.html</echo>
-
-      <!-- check for duplicated code -->
-      <echo>WARNING: use environment variable: ANT_OPTS=-Xmx512m or this task will fail.</echo>
-      <echo>Checking for duplicated code using the Copy/Paste Detector (CPD).</echo>
-      <taskdef name="cpd" classname="net.sourceforge.pmd.cpd.CPDTask" >
-        <classpath>
-          <pathelement path="${project.class.path}" />
-          <fileset dir="${library.directory}">
-            <include name="*.jar" />
-          </fileset>
-        </classpath>
-      </taskdef>
-      <cpd format="text" minimumTokenCount="200" outputFile="${build.directory}/duplicatedCodeReport4EvA2-${DSTAMP}.txt">
-        <fileset dir="${source.directory}">
-            <include name="**/*.java"/>
-        </fileset>
-      </cpd>
-    <echo>result written to ${basedir}/${build.directory}/duplicatedCodeReport4EvA2-${DSTAMP}.txt</echo>
-  </target>
-
-
-  <target name="javancss" depends="init" description="SOFTWAREDESIGN: Determining the NCSS and CCN code metrics for JOELib.">
-    <echo>Starts JavaNCSS ...</echo>
-    <taskdef name="javancss" classname="javancss.JavancssAntTask">
-      <classpath>
-          <pathelement path="${project.class.path}" />
-          <fileset dir="${library.directory}">
-            <include name="*.jar" />
-          </fileset>
-        </classpath>
-    </taskdef>
-    <echo>Cyclomatic
-Complexity             Ease of       Risk
-Number (CCN)           maintenance
-(McCabe metric)
----------------------------------------------
-1-10, simple           easy          minimum
-11-20, complex         moderate      moderate
-21-50, more complex    hard          high
->50, unstable          very hard     very high
-
-</echo>
-     <javancss srcdir="${source.directory}"
-            includes="**/*.java"
-            excludes="jama/**/*.java, jmat/**/*.java, cformat/**/*.java"
-            abortOnFail="false"
-            ccnPerFuncMax="30"
-            generateReport="true"
-            outputfile="${build.directory}/javancssReport4EvA2-${DSTAMP}.txt"
-            format="text"
-            packageMetrics="true"
-            classMetrics="false"
-            functionMetrics="false"
-            />
-    <echo>result written to ${basedir}/${build.directory}/javancssReport4EvA2-${DSTAMP}.txt</echo>
-  </target>
-
-  <target name="jalopy" description="SOFTWAREDESIGN: source code formatter using the JOELib convention.">
-    <taskdef name="jalopy" classname="de.hunsicker.jalopy.plugin.ant.AntPlugin">
-      <classpath refid="project.class.path" />
-    </taskdef>
-    <jalopy classpathref="project.class.path"
-            fileformat="unix"
-            convention="../${source.directory}/jalopy.format.convention.xml"
-            history="file"
-            historymethod="adler32"
-            loglevel="error"
-            threads="2"
-            backup="bak">
-      <fileset dir="${source.directory}">
-        <include name="**/*.java"/>
-      </fileset>
-    </jalopy>
-  </target>
-
-  <target name="vizant" description="SOFTWAREDESIGN: create dependency graph for ANT files for the JOELib project.">
-    <echo>Starts VizANT ...</echo>
-    <taskdef name="vizant" classname="net.sourceforge.vizant.Vizant">
-      <classpath>
-        <pathelement path="${project.class.path}" />
-        <fileset dir="${library.directory}">
-          <include name="*.jar" />
-        </fileset>
-      </classpath>
-    </taskdef>
-    <vizant antfile="ant/build.xml" outfile="${build.directory}/vizant_build.dot">
-      <attrstmt type="node">
-        <attr name="style" value="filled"/>
-        <attr name="shape" value="egg"/>
-        <attr name="color" value="grey90"/>
-      </attrstmt>
-    </vizant>
-    <vizant antfile="ant/build.xml" outfile="${build.directory}/vizant_check.dot">
-      <attrstmt type="node">
-        <attr name="style" value="filled"/>
-        <attr name="shape" value="egg"/>
-        <attr name="color" value="grey90"/>
-      </attrstmt>
-    </vizant>
-    <!-- Here you will need GraphViz at http://www.research.att.com/sw/tools/graphviz/ -->
-<!--
-    <exec executable="dot" ><arg line="-Tsvg ${build.directory}/vizant_build.dot -o ${build.directory}/vizant_build.svg"/></exec>
-    <exec executable="dot" ><arg line="-Tsvg ${build.directory}/vizant_check.dot -o ${build.directory}/vizant_check.svg"/></exec>
--->
-    <echo>result written to ${basedir}/${build.directory}/vizant_build.dot ...</echo>
-    <echo>result written to ${basedir}/${build.directory}/vizant_check.dot.</echo>
-  </target>
-
-  <target name="findbugs.calculate" depends="compile">
-    <taskdef name="findbugs" classname="edu.umd.cs.findbugs.anttask.FindBugsTask">
-      <classpath>
-        <pathelement location="${env.JAVA_HOME}/jre/lib/rt.jar" />
-        <pathelement location="${env.JAVA_HOME}/lib/dt.jar" />
-        <pathelement location="${env.JAVA_HOME}/lib/tools.jar" />
-        <pathelement path="${project.class.path}" />
-        <fileset dir="${library.directory}">
-          <include name="*.jar" />
-        </fileset>
-      </classpath>
-    </taskdef>
-    <property name="findbugs.home" value="${basedir}/lib/findbugs" />
-    <findbugs home="${findbugs.home}"
-              output="xml"
-              outputFile="build/joelib-fb.xml" >
-      <auxClasspath>
-        <pathelement location="${env.JAVA_HOME}/jre/lib/rt.jar" />
-        <pathelement location="${env.JAVA_HOME}/lib/dt.jar" />
-        <pathelement location="${env.JAVA_HOME}/lib/tools.jar" />
-        <pathelement path="${project.class.path}" />
-        <fileset dir="${library.directory}">
-          <include name="*.jar" />
-        </fileset>
-      </auxClasspath>
-      <sourcePath path="${basedir}/${source.directory}" />
-      <class location="${basedir}/${build.directory}" />
-    </findbugs>
-  </target>
-
-  <target name="findbugsGUI">
-    <property name="findbugs.home" value="${basedir}/lib/findbugs" />
-    <java classname="edu.umd.cs.findbugs.gui.FindBugsFrame" fork="yes"
-          dir="${build.directory}">
-      <classpath>
-        <pathelement location="${env.JAVA_HOME}/jre/lib/rt.jar" />
-        <pathelement location="${env.JAVA_HOME}/lib/dt.jar" />
-        <pathelement location="${env.JAVA_HOME}/lib/tools.jar" />
-        <pathelement path="${project.class.path}" />
-        <fileset dir="${library.directory}">
-          <include name="*.jar" />
-        </fileset>
-        <fileset dir="${library.directory}/findbugs/lib">
-          <include name="*.jar" />
-        </fileset>
-      </classpath>
-      <jvmarg value="-Dfindbugs.home=${findbugs.home}"/>
-    </java>
-  </target>
-
-  <target name="findbugs" depends="compile" description="SOFTWAREDESIGN: Run bug detector for JOELib and comfortable GUI to analyze results.">
-    <echo>Starts findBugs ...</echo>
-    <antcall target="findbugs.calculate"/>
-    <echo>result written to ${basedir}/${build.directory}/EvA2-fb.xml, now you can open this file with the findBugs GUI ...</echo>
-    <echo>open with 'File->LoadBugs' then open '${basedir}/${build.directory}/EvA2-fb.xml'.</echo>
-    <antcall target="findbugsGUI"/>
-  </target>
-</project>
-
-<!--+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-   END OF FILE
-++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
diff --git a/ant/check.xml b/ant/check.xml
deleted file mode 100644
index 62f270a9..00000000
--- a/ant/check.xml
+++ /dev/null
@@ -1,110 +0,0 @@
-<!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-   Filename: $RCSfile$
-   Purpose:  Ant build file for EvA2.
-
-             Ant-Download: http://jakarta.apache.org/ant
-             Ant-Manual:   http://jakarta.apache.org/ant/manual/index.html
-
-   Precondition: 1. Ant should be installed.
-                 2. JAVA_HOME environment variable contains the path to JDK1.4 or higher
-                 3. ANT_HOME environment variable contains the path to ant's home directory
-
-   Language: XML
-   Compiler: Ant
-   Authors:  Holger Ulmer
-   Version:  $Revision: 6 $
-             $Date: 2006-01-18 10:53:03 +0100 (Wed, 18 Jan 2006) $
-             $Author: streiche $
-   Copyright (c) Dept. Computer Architecture, University of Tuebingen, Germany
-+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
-
-<project name="EvA2" default="check" basedir=".">
-<!--
-As there are no static libraries any more, not much remains to check... (MK)
--->
-
-<!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-        Library check
-+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
-
-  <target name="binary.libraries.check" >
-	<!--
-    <condition property="library.available.SNNS.windows">
-      <and>
-        <available file="${windows.libraries}/${library.SNNS}.dll" type="file" />
-      </and>
-    </condition>
-    <condition property="library.available.SNNS.unix">
-      <and>
-        <available file="${unix.libraries}/lib${library.SNNS}.so" type="file" />
-      </and>
-    </condition>
-    <condition property="library.available.WSI">
-      <and>
-        <available file="${library.WSI}" type="file" />
-      </and>
-    </condition>
-
-    <condition property="library.available.JCompChem">
-      <and>
-        <available file="${library.JCompChem}" type="file" />
-      </and>
-    </condition>
-
-    <condition property="library.available.JavaNNS">
-      <and>
-        <available file="${library.JavaNNS}" type="file" />
-      </and>
-    </condition>
-    <condition property="library.available.ECJ">
-      <and>
-        <available file="${library.ECJ}" type="file" />
-      </and>
-    </condition>
-    -->
-  </target>
-
-  <target name="source.libraries.check" >
-	<!--
-    <condition property="library.available.WSI">
-      <and>
-        <available file="${library.WSI.ant}/wsi" type="dir" />
-      </and>
-    </condition> 
-	-->
-  </target>
-
-    <target name="binary.libraries.test.SNNS.windows" depends="binary.libraries.check" unless="library.available.SNNS.windows">
-      <echo message="WARNING: ${windows.libraries}/${library.SNNS}.dll not available."/>
-    </target>
-    <target name="binary.libraries.test.SNNS.unix" depends="binary.libraries.check" unless="library.available.SNNS.unix">
-      <echo message="WARNING: ${unix.libraries}/lib${library.SNNS}.so not available."/>
-    </target>
-<!--    <target name="binary.libraries.test.WSI" depends="binary.libraries.check" unless="library.available.WSI">
-      <echo message="WARNING: wsi package not available at ${library.WSI}."/>
-    </target>
-    <target name="binary.libraries.test.JavaNNS" depends="binary.libraries.check" unless="library.available.JavaNNS">
-      <echo message="WARNING: javanns package not available at ${library.JavaNNS}."/>
-    </target>
--->
-    <target name="source.libraries.test.WSI" depends="source.libraries.check" unless="library.available.WSI">
-      <warn message="WSI-RA sources are not available at ${library.WSI.ant}. Do not use 'compileAll' target."/>
-    </target>
-
-
-  <target name="binary.libraries.test"    depends="binary.libraries.test.SNNS.windows,
-                                                   binary.libraries.test.SNNS.unix
-                                                  ">
-  </target>
-
-  <target name="source.libraries.test"    depends="source.libraries.test.WSI
-                                                  ">
-  </target>
-
-	<target name="check" 	depends="binary.libraries.check, source.libraries.check">
-	</target>
-</project>
-
-<!--+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-   END OF FILE
-++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
diff --git a/ant/miniBuild.xml b/ant/miniBuild.xml
deleted file mode 100644
index 888140d7..00000000
--- a/ant/miniBuild.xml
+++ /dev/null
@@ -1,386 +0,0 @@
-<!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-   Filename: $RCSfile$
-   Purpose:  Ant build file for EvA2.
-
-             Ant-Download: http://jakarta.apache.org/ant
-             Ant-Manual:   http://jakarta.apache.org/ant/manual/index.html
-
-   Precondition: 1. Ant should be installed.
-                 2. JAVA_HOME environment variable contains the path to JDK1.5 or higher
-                 3. ANT_HOME environment variable contains the path to ant's home directory
-
-   Language: XML
-   Compiler: Ant
-   Authors:  M.Kronfeld, H.Planatscher, Holger Ulmer, Felix Streichert, Joerg Wegner
-   Version:  $Revision: 284 $
-             $Date: 2007-11-27 14:37:05 +0100 (Tue, 27 Nov 2007) $
-             $Author: mkron $
-   Copyright (c) Dept. Computer Architecture, University of Tuebingen, Germany
-+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
-
-<project name="EvA2" default="compile" basedir="..">
-
-<!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-        Set properties
-+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
-
-  <!-- SET THE DIRECTORY PROPERTIES -->
-	<property name="source.directory"				value="src" />
-	<property name="ant.directory"					value="ant" />
-	<property name="build.directory"				value="build" />
-	<property name="resources.directory"			value="resources" />
-	<property name="library.directory"				value="lib" />
-	<property name="matlabinterface.basedir"		value="resources/MatlabInterface" />
-	<property name="matlabinterface.title"			value="JEInterface" />
-	<property name="distribution.directory"			value="dist" />
-	<property name="source.distribution.directory"	value="${distribution.directory}/src-dist" />
-	<property name="binary.distribution.directory"	value="${distribution.directory}/bin-dist" />
-	<property name="javadoc.directory"				value="doc/api" />
-	<property name="jar.name"						value="EvA2Base" />
-	<property name="srcpack.name"					value="EvA2BaseSrc" />
-	<!-- SET THESE PATHES IF YOU WANT TO COMPILE ADDITIONAL EvA2 PACKAGES -->
-	<property name="JE2Probs.directory"				value="../JE2Probs" />	
-	<property name="JE2ESModel.directory"			value="../JE2ESModel" />			
-	<property name="JE2Research.directory"			value="../JE2Research" />
-	
-	<condition property="JE2Probs.available" else="false">
-		<available file="${JE2Probs.directory}"/>
-	</condition>
-	<condition property="JE2ESModel.available" else="false">
-		<available file="${JE2ESModel.directory}"/>
-	</condition>
-	<condition property="JE2Research.available" else="false">
-		<available file="${JE2Research.directory}"/>
-	</condition>
-
-	<!-- SET THE JAVA BINARY LIBRARIES PROPERTIES -->
-	<property name="ant.java.version"							 value="1.5" />
-
-	<!-- SET CLASSPATH -->
-	<path id="project.class.path">
-		<pathelement location="." />
-	</path>
-
-	<!-- ENVIRNONMENT PROPERTIES -->
-	<property environment="env"/>
-
-<!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-        Usage
-+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
-
-  <target name="usage" unless="silent">
-    <echo>
-      Supported targets (default=compile):
-      -------------------------------------------------------------------------
-      compile    - compile project files of the base package.
-      compileAll - compile project file of all packages
-      binaryDist - create a binary distribution of the base package
-      sourceDist - create a source distribution of the base package
-      clean      - clean up files, except the source files and the api
-                   documentation
-      run        - will start EvA2
-
-      use 'ant -projecthelp' for further Main targets
-    </echo>
-  </target>
-
-<!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-        Init
-+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
-
-  <target name="buildDirectories" unless="noDirectories">
-    <mkdir dir="${build.directory}" />
-    <mkdir dir="${distribution.directory}" />
-    <mkdir dir="${source.distribution.directory}" />
-    <mkdir dir="${binary.distribution.directory}" />
-    <mkdir dir="${javadoc.directory}" />
-  </target>
-
-  <target name="init">
-    <tstamp />
-    <antcall target="buildDirectories"></antcall>
-    <condition property="isWindows">
-      <and>
-        <os family="windows" />
-        <not>
-          <os family="unix" />
-        </not>
-      </and>
-    </condition>
-    <condition property="isUnix">
-      <and>
-        <os family="unix" />
-        <not>
-          <os family="windows" />
-        </not>
-      </and>
-    </condition>
-  </target>
-
-<!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-        Clean
-+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
-
-  <target name="clean" description="Cleans up project directories.">
-    <delete dir="${build.directory}" />
-    <delete dir="${distribution.directory}" />
-  </target>
-
-	<!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-		        Clean JE2Probs
-	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
-		<target name="cleanProbs" depends="usage, init, compileInfo" description="Compiles the Probs project." if="JE2Probs.available">
-		  	<ant inheritAll="false" antfile="${ant.directory}/build.xml" dir="${JE2Probs.directory}" target="clean">
-				<property name="silent" value="true"/>
-			</ant>
-		</target>
-		
-	<!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-		      Clean JE2ESModel
-	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
-		<target name="cleanESModel" depends="usage, init, compileInfo" description="Compiles the ESModel project." if="JE2ESModel.available">
-		  	<ant inheritAll="false" antfile="${ant.directory}/build.xml" dir="${JE2ESModel.directory}" target="clean">
-				<property name="silent" value="true"/>
-			</ant>
-		</target>
-			
-  <target name="cleanAll" depends="init, clean, cleanProbs, cleanESModel">
-  </target>
-
-<!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-        CompileAll
-+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
-
-  <target name="compileAll" depends="compile, compileProbs, compileESModel, compileResearch" description="Update libraries and compile the project.">
-  </target>
-	
-<!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-	        Compile Information
-+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
-  <target name="compileInfo" unless="silent">
-    <echo message="JE2Base Project"/>
-    <echo message="ANT_HOME is set to = ${env.ANT_HOME}"/>
-    <echo message="JAVA_HOME is set to = ${env.JAVA_HOME}"/>
-    <echo message="You are using JDK version ${ant.java.version}."/>
-    <echo message=""/>
-    <echo message="use 'ant compileAll' - to compile all packages."/>
-    <echo message="use 'ant compile'    - to compile only the base package."/>
-  	<echo message="JE2Probs available: ${JE2Probs.available}" />
-  	<echo message="JE2ESModel available: ${JE2ESModel.available}" />
- 	<echo message="JE2Research available: ${JE2Research.available}" />
-  </target>
-
-  <target name="compile" depends="usage, init, compileInfo" description="Compiles the project." >
-  <!-- COMPILE PROJECT -->
-  <javac destdir="${build.directory}" optimize="on" deprecation="on" nowarn="on" debug="${debug.flag}" >
-     <src path="${source.directory}" />
-     <exclude name="ant/**" />
-     <exclude name="build/**" />
-     <exclude name="dist/**" />
-     <exclude name="doc/**" />
-     <exclude name="resources/**" />
-     <exclude name="images/**" />
-     <exclude name="lib/**" />
-     <exclude name="project/**" />
-	 <classpath>
-       <pathelement path="${project.class.path}" />
-     </classpath>
-   </javac>
-
-   <!-- GENERATE RMI STUB FILES -->
-   <rmic includes="eva2/tools/jproxy/RMIInvocationHandlerImpl.class"       stubversion="-v1.2" base="${build.directory}"/>
-   <rmic includes="eva2/tools/jproxy/RMIThreadInvocationHandlerImpl.class" stubversion="-v1.2" base="${build.directory}"/>
-
-   <!-- COPY DATA FILES TO BUILD DIRECTORY -->
-    <copy todir="${build.directory}/resources">
-      <fileset dir="${resources.directory}" includes="**/*">
-        <exclude name="**/*.xcf" />
-      </fileset>
-   </copy>
-  </target>
-	
-<!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-	        Compile JE2Probs
-+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
-	<target name="compileProbs" depends="usage, init, compileInfo" description="Compiles the Probs project." if="JE2Probs.available">
-	  	<ant inheritAll="false" antfile="${ant.directory}/build.xml" dir="${JE2Probs.directory}" target="compile">
-			<property name="silent" value="true"/>
-		</ant>
-	</target>
-	
-<!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-	        Dist JE2Probs
-+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
-	<target name="distProbs" depends="compileProbs" description="Build dist. of the Probs project." if="JE2Probs.available">
-	  	<ant inheritAll="false" antfile="${ant.directory}/build.xml" dir="${JE2Probs.directory}" target="dist">
-			<property name="silent" value="true"/>
-		</ant>
-	</target>
-	
-<!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-	      Compile JE2ESModel
-+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
-	<target name="compileESModel" depends="usage, init, compileInfo" description="Compiles the ESModel project (if available)." if="JE2ESModel.available">
-	  	<ant inheritAll="false" antfile="${ant.directory}/build.xml" dir="${JE2ESModel.directory}" target="compile">
-			<property name="silent" value="false"/>
-		</ant>
-	</target>
-
-<!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-	        Dist JE2ESModel
-+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
-	<target name="distESModel" depends="compileESModel" description="Build dist. of the ESModel project (if available)." if="JE2Probs.available">
-	  	<ant inheritAll="false" antfile="${ant.directory}/build.xml" dir="${JE2ESModel.directory}" target="dist">
-			<property name="silent" value="true"/>
-		</ant>
-	</target>
-	
-<!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-	      Compile JE2Research
-+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
-	<target name="compileResearch" depends="usage, init, compileInfo" description="Compiles the Research project (if available)." if="JE2Research.available">
-	 	<ant inheritAll="false" antfile="${ant.directory}/build.xml" dir="${JE2Research.directory}" target="compile">
-			<property name="silent" value="false"/>
-		</ant>
-	</target>
-		
-<!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-        Binary Distribution
-+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
-<target name="binaryDist" depends="compile, JEInterface" description="Compiles the project and builds a jar-file.">
-    <property name="bin.dist.dir"  value="${binary.distribution.directory}/eva-${DSTAMP}" />
-    <mkdir dir="${bin.dist.dir}" />
-	<delete>
-      <fileset dir="${bin.dist.dir}/" includes="${jar.name}.jar" />
-	</delete>
-
-	<jar jarfile="${bin.dist.dir}/${jar.name}.jar"  basedir="${build.directory}" >
-	  <manifest> <attribute name="Main-Class" value="eva2.gui.Main"/> </manifest>
-	</jar>
-	
-    <copy todir="${distribution.directory}">
-      <fileset dir="${bin.dist.dir}">
-        <include name="${jar.name}.jar" />
-      </fileset>
-    </copy>
-  </target>
-
-<!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-        Source Distribution
-+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
-
-  <target name="sourceDist" depends="init">
-    <property name="src.dist.dir"  value="${source.distribution.directory}/eva2-${DSTAMP}" />
-    <mkdir dir="${src.dist.dir}" />
-    <copy todir="${src.dist.dir}/${source.directory}">
-      <fileset dir="${source.directory}">
-      	<include name="**/*java" />
-      	<include name="**/*txt" />
-      </fileset>
-    </copy>
-    <copy todir="${src.dist.dir}/${resources.directory}">
-      <fileset dir="${resources.directory}">
-      	<include name="**/**" />
-      </fileset>
-    </copy>
-    <mkdir dir="${src.dist.dir}/${library.directory}" />
-    <copy todir="${src.dist.dir}/${library.directory}">
-      <fileset dir="${library.directory}" includes="**jar" />
-    </copy>
-    <tar tarfile="${distribution.directory}/${srcpack.name}.tar"
-         basedir="${src.dist.dir}" includes="**" excludes="*.tar*, *.zip"/>
-    <gzip zipfile="${distribution.directory}/${srcpack.name}.tar.gz"
-          src="${distribution.directory}/${srcpack.name}.tar" />
-    <delete file="${distribution.directory}/${srcpack.name}.tar" />
-
-    <zip zipfile="${distribution.directory}/${srcpack.name}.zip">
-      <zipfileset dir="${src.dist.dir}">
-        <include name="**" />
-        <exclude name="*.tar*, *.zip" />
-      </zipfileset>
-    </zip>
-  </target>
-
-<!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-        Generate Distribution
-+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
-
-  <target name="dist" depends="distESModel, distProbs, binaryDist, sourceDist" description="Builds all distributions if all packages are available.">
-  </target>
-	
-	<!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-	        Matlab Interface tar.gz to the distribution dir.
-	+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
-
-  <target name="JEInterface">
-    <tar tarfile="${matlabinterface.basedir}/${matlabinterface.title}.tar"
-         basedir="${matlabinterface.basedir}" includes="**" excludes="*.tar*, *.zip"/>
-  	
-    <gzip zipfile="${matlabinterface.basedir}/${matlabinterface.title}.tar.gz"
-          src="${matlabinterface.basedir}/${matlabinterface.title}.tar" />
-    <copy todir="${distribution.directory}">
-  	  <fileset dir="${matlabinterface.basedir}">
-  		<include name="${matlabinterface.title}.tar.gz" />
-  	  </fileset>
-  	</copy>
-  	<delete file="${matlabinterface.basedir}/${matlabinterface.title}.tar" />
-  	<delete file="${matlabinterface.basedir}/${matlabinterface.title}.tar.gz" />
-  	  	  	
-  </target>
-
-<!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-        Run EvA2
-+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
-
-  <target name="run" description="Runs EvA2.">
-    <java classname="eva2.gui.Main" fork="yes">
-      <jvmarg value="-Xmx512m"/>
-      <classpath>
-      	<pathelement path="${project.class.path}" />
-      	<pathelement path="${build.directory}" />
-      	</classpath>
-    </java>
-  </target>
-
-<!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-        Javadoc - Unfortunately the java documentation is a bit of a mess. Also check the GUI tip texts.
-+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
-
-  <target name="javadoc" description="Generates the JavaDoc-API Documentation.">
-    <javadoc packagenames="eva2.*"
-    windowtitle ="EvA2 API Documentation"
-    doctitle    ="EvA2 API Documentation"
-    author      ="true"
-    version     ="true"
-    use         ="true"
-    destdir="${javadoc.directory}"
-    private     ="true">
-            <classpath refid="project.class.path" />
-            <sourcepath>
-              <pathelement path="${source.directory}" />
-            </sourcepath>
-            <doctitle><![CDATA[<h1>Test</h1>]]></doctitle>
-
-            <header><![CDATA[<font size="-1"><b><i>
-                             <A HREF="http://www.ra.cs.uni-tuebingen.de/software/EvA2/index.html"
-                                target="_top">EvA2
-                             </A>
-                             </b></i></font>]]>
-            </header>
-
-        <footer><![CDATA[eva2<br>
-                         <A HREF="http://www.ra.cs.uni-tuebingen.de/software/EvA2/index.html"
-                            target="_top">EvA2
-                         </A>]]>
-        </footer>
-            <link offline="true"
-                  href="http://java.sun.com/j2se/jdk1.5.0_03/docs/api/"
-                  packagelistLoc="${env.JAVA_HOME}/docs/api"
-            />
-            <link href="http://developer.java.sun.com/developer/products/xml/docs/api/"/>
-    </javadoc>
-  </target>
-</project>
-<!--+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-   END OF FILE
-++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->