diff --git a/benchmarking/build.xml b/benchmarking/build.xml
index 1c67f651a..1d4479222 100644
--- a/benchmarking/build.xml
+++ b/benchmarking/build.xml
@@ -1,77 +1,24 @@
 <?xml version="1.0"?>
 <project name="org.bridgedb.tools.benchmarking" default="jar" basedir=".">
-	
-	<path id="project.class.path">
-		<pathelement location="build"/>
-		<fileset dir="lib">
-			<include name="*.jar"/>
-		</fileset>
-		<pathelement location="../dist/org.bridgedb.jar"/>
-		<pathelement location="../dist/derby.jar"/>
-		<!--TODO make sure corelib build is called first -->
-	</path>
 
-	<path id="class.path">
-		<fileset dir="../dist">
-			<include name="*.jar"/>
+	<import file="../build-common.xml" />
+
+	<path id="absolute.deps">
+		<fileset dir="${bundle.dest}">
+			<include name="org.bridgedb.jar"/>
+			<include name="org.bridgedb.bio.jar"/>
+			<include name="org.bridgedb.server.jar"/>
+			<include name="derby.jar"/>
 		</fileset>
-		<fileset dir="lib">
-			<include name="*.jar"/>
+		<fileset dir="../common-bundles">
+			<include name="com.google.collect*.jar"/>
 		</fileset>
 	</path>
 
-	<target name="prepare">
-		<mkdir dir="build"/>
-	</target>
-	
-	<target name="clean" description="Remove all generated files.">
-		<delete dir="${build.dir}"/>
-	</target>
-	
-	<target name="build" depends="prepare" description="Compile all sources">
-		<javac srcdir="src" 
-			    debug="true"	
-			    destdir="build">
-			<classpath refid="class.path"/>
-		</javac>
-	</target>
-	
-	<target name="jar" depends="build">
-		<mkdir dir="dist"/>
-		<jar jarfile="dist/checker.jar">
-			<manifest>
-				<attribute name="Main-Class" value="org.bridgedb.checker.Checker"/>
-				<attribute name="Class-Path" value="bridgedb.jar google-collect-snapshot-20080820.jar"/>
-			</manifest>
-			<fileset dir="build" includes="**/*.class"/>
-		</jar>
-	</target>
-	
-	<target name="dist" depends="jar"/>
-
-	<target name="test" depends="build">
-		<path id="test.classpath">
-			<path refid="class.path"/>
-			<pathelement location="build"/>
-			<pathelement location="../corelib/build-lib/junit.jar"/>
-			<pathelement location="../corelib/build-lib/measure.jar"/>
-			<pathelement location="../corelib/build-lib/derbyclient.jar"/>
-		</path>
-		<javac srcdir="test" debug="true" 
-					includes="**"
-					destdir="build"
-					source="1.5">
-			<classpath refid="test.classpath"/>
-		</javac>		
-		<junit printsummary="on" haltonfailure="false" fork="true">
-			<formatter type="brief" usefile="false"/>
-			<classpath refid="test.classpath"/>
-			<batchtest>
-				<fileset dir="test">
-					<include name="**/*Test*.java"/>
-				</fileset>
-			</batchtest>
-		</junit>
-	</target>
+	<path id="test.deps">
+		<pathelement location="../corelib/build-lib/junit.jar"/>
+		<pathelement location="../corelib/build-lib/measure.jar"/>
+		<pathelement location="../corelib/build-lib/derbyclient.jar"/>
+	</path>
 	
 </project>
diff --git a/build-common.xml b/build-common.xml
index 601154035..56651df01 100644
--- a/build-common.xml
+++ b/build-common.xml
@@ -5,14 +5,15 @@
 
 	<property file="version.props"/>
 
+	<!-- Override this to put the jars in a different target directory -->
 	<property name="bundle.dest" value="../dist"/>
 
 	<target name="prepare-jar-name">
-		<!-- the name of the plug-in jar uses the project name of the calling build file -->
+		<!-- the name of the plug-in jar is the project name of the calling build file with '.jar' appended -->
 		<property name="jar.name" value="${bundle.dest}/${ant.project.name}.jar"/>
 	</target>
 
-	<target name="prepare-common">
+	<target name="prepare-common" depends="prepare-jar-name">
 		<mkdir dir="build"/>
 
 		<!-- the following property is used to skip the "test" target if there is no test subdirectory -->
@@ -28,7 +29,7 @@
 
 	<target name="prepare"/> <!-- designed to be overriden by project build file -->
 
-	<target name="build" depends="prepare, prepare-common, prepare-jar-name">
+	<target name="build" depends="prepare, prepare-common">
 		<javac srcdir="src"
 			   includes="**"
 			   debug="true"
@@ -37,7 +38,7 @@
 		</javac>
 	</target>
 
-	<!-- if the embed.jars property is specified, unjar those jars into the build directory -->
+	<!-- if the embed.jars property is specified, those jars will be unjarred into the build directory -->
 	<target name="unjar-embedded" depends="build">
 		<unjar dest="build">
 			<path refid="embed.jars"/>
@@ -46,15 +47,23 @@
 	
 	<target name="jar-common" depends="build, unjar-embedded"> 
 		<echo>Creating JAR: ${jar.name}</echo>
-		<manifestclasspath property="manifest.cp" jarfile="${jar.name}">
-			<classpath>
-				<path refid="absolute.deps"/>
-				<path refid="transient.deps"/>
-			</classpath>
-		</manifestclasspath>
+		
+		<!-- convert classpath to a flat list/string for use as manifest classpath. 
+		We want a flat list, assuming all jars will end up in the same destination dir.
+		We can't use the manifestclasspath task for this, because it will try to figure 
+		out relative paths, which is not what we want because the jars are not in their 
+		final location -->
+		<pathconvert property="manifest.cp" pathsep=" ">
+			<path refid="absolute.deps"/>
+			<path refid="transient.deps"/>
+			<flattenmapper />
+		</pathconvert>
+		<!-- In eclipse, you need create a Bundle-ClassPath entry in MANIFEST.MF for each non-OSGI jar.
+		This causes trouble if we are running outside eclipse, because the jars usually end up in a different location.
+		The trick is to remove the bundle-classpath used by eclipse, we embed these jars instead -->
 		<copy file="META-INF/MANIFEST.MF" toDir="build/META-INF"/>
-		<!-- The trick is to ignore the bundle-classpath used by eclipse, we embed these jars instead -->
 		<replaceregexp file="build/META-INF/MANIFEST.MF" match="^Bundle-ClassPath:" replace="Ignore-this:" flags="m"/>
+		<!-- Finally, create the jar file. Include all resources, build results, and manifest. -->
 		<jar jarfile="${jar.name}" manifest="META-INF/MANIFEST.MF">
 			<manifest>
 				<attribute name="Class-Path" value="${manifest.cp}"/>
@@ -70,22 +79,24 @@
 
 	<target name="jar" depends="jar-common"/> <!-- may be overriden by project build file -->
 
+	<!-- just removes class files -->
 	<target name="clean">
 		<delete dir="build"/>
 	</target>
 
+	<!-- removes class files and generated jar -->
 	<target name="dist-clean" depends="clean, prepare-jar-name">
 		<delete file="${jar.name}"/>
 	</target>
 
+	<!-- creates the jar, and also places all dependencies in the bundle dest directory -->
 	<target name="dist" depends="jar">
-		<copy todir="../dist">
-			<fileset dir="lib" erroronmissingdir="false">
-				<include name="*.jar"/>
-			</fileset>
+		<copy todir="${bundle.dest}">
+			<path refid="absolute.deps"/>
 		</copy>
 	</target>
 
+	<!-- run all junit tests found in the test directory -->
 	<target name="test" depends="build" if="test.dir.exists">
 		<path id="test.classpath">
 			<path refid="absolute.deps"/>
diff --git a/dbbuilder/build.xml b/dbbuilder/build.xml
index 09fa370f8..f8806f345 100644
--- a/dbbuilder/build.xml
+++ b/dbbuilder/build.xml
@@ -1,20 +1,21 @@
 <?xml version="1.0"?>
 <project name="org.bridgedb.tools.dbbuilder" default="jar" basedir=".">
 
+	<import file="../build-common.xml" />
+
 	<!-- absolute deps are used for building, testing and in the manifest classpath -->
-  <path id="absolute.deps">
-    <pathelement location="../dist/org.bridgedb.jar"/>
-    <pathelement location="../dist/org.bridgedb.bio.jar"/>
-    <pathelement location="../dist/org.bridgedb.rdb.jar"/>
-    <pathelement location="../dist/org.bridgedb.rdb.construct.jar"/>
-  </path>  
+	<path id="absolute.deps">
+		<fileset dir="${bundle.dest}">
+			<include name="org.bridgedb.jar"/>
+			<include name="org.bridgedb.bio.jar"/>
+			<include name="org.bridgedb.rdb.jar"/>
+			<include name="org.bridgedb.rdb.construct.jar"/>
+		</fileset>
+	</path>  
 
 	<!-- embedded jars are embedded in the resulting bundle -->
 	<path id="embed.jars">
 		<!-- None -->
 	</path>
 
-  <import file="../build-common.xml" />
-
-
 </project>
diff --git a/org.bridgedb.bio/build.xml b/org.bridgedb.bio/build.xml
index 19f8d19b1..a20629eb4 100644
--- a/org.bridgedb.bio/build.xml
+++ b/org.bridgedb.bio/build.xml
@@ -1,9 +1,11 @@
 <?xml version="1.0"?>
 <project name="org.bridgedb.bio" default="dist" basedir=".">
-	
+
+	<import file="../build-common.xml" />
+
 	<!-- absolute deps are used for building, testing and in the manifest classpath -->
 	<path id="absolute.deps">
-		<pathelement location="../dist/org.bridgedb.jar"/>
+		<pathelement location="${bundle.dest}/org.bridgedb.jar"/>
 	</path>
 
 	<!-- transient deps are optional, they are used only in the manifest classpath -->
@@ -22,6 +24,4 @@
 		<pathelement location="../org.bridgedb/build-lib/hamcrest-core.jar"/>
 	</path>
 
-	<import file="../build-common.xml" />
-
 </project>
diff --git a/org.bridgedb.file.orthoxml/build.xml b/org.bridgedb.file.orthoxml/build.xml
index 60b5a2280..fd942ff09 100644
--- a/org.bridgedb.file.orthoxml/build.xml
+++ b/org.bridgedb.file.orthoxml/build.xml
@@ -1,9 +1,11 @@
 <?xml version="1.0"?>
 <project name="org.bridgedb.file.orthoxml" default="dist" basedir=".">
+
+	<import file="../build-common.xml" />
 	
 	<!-- absolute deps are used for building, testing and in the manifest classpath -->
 	<path id="absolute.deps">
-		<fileset dir="../dist">
+		<fileset dir="${bundle.dest}">
 			<include name="org.bridgedb.jar"/>
 			<include name="org.bridgedb.bio.jar"/>
 		</fileset>
@@ -24,6 +26,4 @@
 		<pathelement location="../org.bridgedb/build-lib/junit4.jar"/>
 	</path>
 
-	<import file="../build-common.xml" />
-
 </project>
diff --git a/org.bridgedb.gui/build.xml b/org.bridgedb.gui/build.xml
index 0c2aaf129..2d8ea52a0 100644
--- a/org.bridgedb.gui/build.xml
+++ b/org.bridgedb.gui/build.xml
@@ -1,9 +1,11 @@
 <?xml version="1.0"?>
 <project name="org.bridgedb.gui" default="dist" basedir=".">
-	
+
+	<import file="../build-common.xml" />
+
 	<!-- absolute deps are used for building, testing and in the manifest classpath -->
 	<path id="absolute.deps">
-		<fileset dir="../dist">
+		<fileset dir="${bundle.dest}">
 			<include name="org.bridgedb.jar"/>
 			<include name="org.bridgedb.webservice.bridgerest.jar"/>
 			<include name="org.bridgedb.rdb.jar"/>
@@ -26,6 +28,4 @@
 		<pathelement location="../org.bridgedb/build-lib/hamcrest-core.jar"/>
 	</path>
 
-	<import file="../build-common.xml" />
-
 </project>
diff --git a/org.bridgedb.rdb.construct/build.xml b/org.bridgedb.rdb.construct/build.xml
index 93e3435f5..a305c8de6 100644
--- a/org.bridgedb.rdb.construct/build.xml
+++ b/org.bridgedb.rdb.construct/build.xml
@@ -1,9 +1,11 @@
 <?xml version="1.0"?>
 <project name="org.bridgedb.rdb.construct" default="dist" basedir=".">
+
+	<import file="../build-common.xml" />
 	
 	<!-- absolute deps are used for building, testing and in the manifest classpath -->
 	<path id="absolute.deps">
-		<fileset dir="../dist">
+		<fileset dir="${bundle.dest}">
 			<include name="org.bridgedb.jar"/>
 			<include name="org.bridgedb.bio.jar"/>
 			<include name="org.bridgedb.rdb.jar"/>
@@ -12,7 +14,9 @@
 
 	<!-- transient deps are optional, they are used only in the manifest classpath -->
 	<path id="transient.deps">
-		<pathelement location="lib/derby.jar"/>
+		<fileset dir="${bundle.dest}">
+			<include name="derby.jar"/>
+		</fileset>
 	</path>
 
 	<!-- embedded jars are embedded in the resulting bundle -->
@@ -25,6 +29,4 @@
 		<!-- nothing yet... -->
 	</path>
 
-	<import file="../build-common.xml" />
-
 </project>
diff --git a/org.bridgedb.rdb/build.xml b/org.bridgedb.rdb/build.xml
index 576d7f28c..7f632642f 100644
--- a/org.bridgedb.rdb/build.xml
+++ b/org.bridgedb.rdb/build.xml
@@ -1,9 +1,11 @@
 <?xml version="1.0"?>
 <project name="org.bridgedb.rdb" default="dist" basedir=".">
+
+	<import file="../build-common.xml" />
 	
 	<!-- absolute deps are used for building, testing and in the manifest classpath -->
 	<path id="absolute.deps">
-		<fileset dir="../dist">
+		<fileset dir="${bundle.dest}">
 			<include name="org.bridgedb.jar"/>
 			<include name="org.bridgedb.bio.jar"/>
 		</fileset>
@@ -11,7 +13,9 @@
 
 	<!-- transient deps are optional, they are used only in the manifest classpath -->
 	<path id="transient.deps">
-		<pathelement location="lib/derby.jar"/>
+		<fileset dir="${bundle.dest}">
+			<include name="derby.jar"/>
+		</fileset>
 	</path>
 
 	<!-- embedded jars are embedded in the resulting bundle -->
@@ -27,6 +31,4 @@
 		<pathelement location="build-lib/derbyclient.jar"/>
 	</path>
 
-	<import file="../build-common.xml" />
-
 </project>
diff --git a/org.bridgedb.server/build.xml b/org.bridgedb.server/build.xml
index b7e4c6115..557251808 100644
--- a/org.bridgedb.server/build.xml
+++ b/org.bridgedb.server/build.xml
@@ -1,11 +1,15 @@
 <?xml version="1.0"?>
 <project name="org.bridgedb.server" default="dist" basedir=".">
 
+	<import file="../build-common.xml" />
+
 	<!-- absolute deps are used for building, testing and in the manifest classpath -->
 	<path id="absolute.deps">
-		<pathelement location="../dist/org.bridgedb.jar"/>
-		<pathelement location="../dist/org.bridgedb.bio.jar"/>
-		<pathelement location="../dist/org.bridgedb.rdb.jar"/>
+		<fileset dir="${bundle.dest}">
+			<include name="org.bridgedb.jar"/>
+			<include name="org.bridgedb.bio.jar"/>
+			<include name="org.bridgedb.rdb.jar"/>
+		</fileset>
 	</path>
 
 	<!-- transient deps are optional, they are used only in the manifest classpath -->
@@ -24,16 +28,16 @@
 		<pathelement location="../org.bridgedb/build-lib/junit.jar"/>
 	</path>
 
+  <!-- override main class and classpath in manifest -->
+  <target name="jar" depends="jar-common">
+	<jar jarfile="${jar.name}" update="true">
+	  <manifest>
+		<attribute name="Main-Class" value="org.bridgedb.server.Server"/>
+		<attribute name="Class-Path" value="derby.jar org.bridgedb.jar org.bridgedb.bio.jar org.bridgedb.rdb.jar org.restlet.jar commons-cli-1.2.jar"/>
+	  </manifest>
+	</jar>
+  </target>
   
-	<target name="jar" depends="build">
-		<jar jarfile="${jar.name}" update="true">
-		  <manifest>
-			<attribute name="Main-Class" value="org.bridgedb.server.Server"/>
-			<attribute name="Class-Path" value="derby.jar org.bridgedb.jar org.bridgedb.bio.jar org.bridgedb.rdb.jar org.restlet.jar commons-cli-1.2.jar"/>
-		  </manifest>
-		</jar>
-	</target>
-
 	<target name="war" depends="jar">
 		<fail message="You must specify the bridgedb config file that specifies the database locations for the web application. Example: ant war -Dbridge.config=/home/thomas/data/bridgedb/bridge.config.">
 			<condition>
@@ -61,6 +65,4 @@
 		<!-- Disabled for now... -->
 	</target>
 
-	<import file="../build-common.xml" />
-
 </project>
diff --git a/org.bridgedb.tools.batchmapper/build.xml b/org.bridgedb.tools.batchmapper/build.xml
index 168cd22df..5cf880f54 100644
--- a/org.bridgedb.tools.batchmapper/build.xml
+++ b/org.bridgedb.tools.batchmapper/build.xml
@@ -1,9 +1,11 @@
 <?xml version="1.0"?>
 <project name="org.bridgedb.tools.batchmapper" default="jar" basedir=".">
-		
+
+	<import file="../build-common.xml" />
+
 	<!-- absolute deps are used for building, testing and in the manifest classpath -->
 	<path id="absolute.deps">
-		<fileset dir="../dist">
+		<fileset dir="${bundle.dest}">
 			<include name="org.bridgedb.jar"/>
 			<include name="org.bridgedb.bio.jar"/>
 		</fileset>
@@ -11,7 +13,7 @@
 
 	<!-- transient deps are optional, they are used only in the manifest classpath -->
 	<path id="transient.deps">
-		<fileset dir="../dist">
+		<fileset dir="${bundle.dest}">
 			<include name="derby.jar"/>
 			<include name="org.bridgedb.rdb.jar"/>
 		</fileset>
@@ -36,6 +38,4 @@
 		</jar>
 	</target>
 
-	<import file="../build-common.xml" />
-
 </project>
diff --git a/org.bridgedb.tools.miriam/build.xml b/org.bridgedb.tools.miriam/build.xml
index 2ee7097ed..e0e846b49 100644
--- a/org.bridgedb.tools.miriam/build.xml
+++ b/org.bridgedb.tools.miriam/build.xml
@@ -1,90 +1,62 @@
 <?xml version="1.0"?>
 <project name="org.bridgedb.tools.miriam" default="dist" basedir=".">
-  
-  <target name="prepare">
-	<mkdir dir="build"/>
-  </target>
 
-  <path id="dependencies">
-	<fileset dir="../lib" includes="*jdom*.jar" />
-	<fileset dir="../org.bridgedb.webservice.cronos/lib/axis-1_4/lib" includes="*.jar" />
-  </path>
-  
-  <path id="class.path">
-    <path refid="dependencies"/>
-    <fileset dir="../dist">
-      <include name="org.bridgedb.jar"/>
-      <include name="org.bridgedb.bio.jar"/>
-    </fileset>
-  </path>
+	<import file="../build-common.xml" />
 
-  <target name="build" depends="prepare">
-	<javac srcdir="src-axis"
-		   includes="**"
-		   debug="true"
-		   destdir="build">
-		<classpath refid="class.path"/>
-	</javac>
-    <javac srcdir="src"
-		   includes="**"
-		   debug="true"
-		   destdir="build">
-		<classpath refid="class.path"/>
-	</javac>
-    <copy toDir="../dist"><path refid="dependencies"/></copy>
-  </target>
-  
-  <target name="jar" depends="build">
-	<jar jarfile="${jar.name}">
-	  <fileset dir="build" includes="**/*.class"/>
+	<!-- embedded jars are embedded in the resulting bundle -->
+	<path id="embed.jars">
+		<fileset dir="../org.bridgedb.webservice.cronos/lib/axis-1_4/lib" includes="*.jar" />
+	</path>
+
+	<path id="absolute.deps">
+		<fileset dir="../dist">
+		  <include name="org.bridgedb.jar"/>
+		  <include name="org.bridgedb.bio.jar"/>
+		</fileset>
+		<fileset dir="../common-bundles" includes="*jdom*.jar" />
+	</path>
+
+	<!-- transient deps are optional, they are used only in the manifest classpath -->
+	<path id="transient.deps">
+	</path>
+
+	<!-- overrides build target in common build file -->
+	<target name="build" depends="prepare, prepare-common">
+		<javac srcdir="src-axis"
+			   includes="**"
+			   debug="true"
+			   destdir="build">
+			   <classpath>
+					<path refid="embed.jars"/>
+				</classpath>
+		</javac>
+		<javac srcdir="src"
+			   includes="**"
+			   debug="true"
+			   destdir="build">
+			   <classpath>
+					<path refid="embed.jars"/>
+					<path refid="absolute.deps"/>
+				</classpath>
+		</javac>
+	</target>
+
+  <!-- overrides jar target in common build file -->
+  <target name="jar" depends="jar-common">
+	<jar jarfile="${jar.name}" update="true">
 	  <manifest>
 		<attribute name="Main-Class" value="org.bridgedb.tools.miriam.UpdateDatasources"/>
-		<attribute name="Class-Path" value="org.bridgedb.jar org.bridgedb.bio.jar axis.jar commons-discovery-0.2.jar log4j-1.2.8.jar jaxrpc.jar saaj.jar wsdl4j-1.5.1.jar commons-logging-1.0.4.jar com.springsource.org.jdom-1.1.0.jar"/>
+<!--		<attribute name="Class-Path" value="org.bridgedb.jar org.bridgedb.bio.jar axis.jar commons-discovery-0.2.jar log4j-1.2.8.jar jaxrpc.jar saaj.jar wsdl4j-1.5.1.jar commons-logging-1.0.4.jar com.springsource.org.jdom-1.1.0.jar"/> -->
 	  </manifest>
 	</jar>
   </target>
 
-  <target name="clean">
-	<delete dir="build"/>
-	<delete dir="doc"/>
-  </target>
-
-  <target name="dist-clean" depends="clean">
-	<delete file="${jar.name}"/>
-  </target>
-
-  <target name="dist" depends="jar"/>
-			 
-	<target name="test" depends="build">
-		<path id="test.classpath">
-			<path refid="class.path"/>
-			<pathelement location="build"/>
-			<pathelement location="../org.bridgedb/build-lib/junit.jar"/>
-			<pathelement location="../org.bridgedb/build-lib/measure.jar"/>
-		</path>
-		<javac srcdir="test" debug="true" 
-					includes="**"
-					destdir="build"
-					source="1.5">
-			<classpath refid="test.classpath"/>
-		</javac>		
-		<junit printsummary="on" haltonfailure="true" fork="true">
-			<formatter type="brief" usefile="false"/>
-			<classpath refid="test.classpath"/>
-			<batchtest>
-				<fileset dir="test">
-					<include name="**/*Test*.java"/>
-				</fileset>
-			</batchtest>
-		</junit>
-	</target>
-
 	<property name="wsdl.url" value="http://www.ebi.ac.uk/miriamws/main/MiriamWebServices?wsdl"/>
 	<property name="src.axis" value="src-axis"/>
 	<property name="build.wpclient.dir" value="build/wpclient" />
 	
 	<target name="update-axis">
-		<fail message="You must specify a url to the CRONOS web service WSDL: 
+		<fail message="You must specify a url to the MIRIAM web service WSDL: 
 			ant -Dwsdl.url=http://www.ebi.ac.uk/miriamws/main/MiriamWebServices?wsdl [ant target]">
 			<condition>
 				<not> <isset property="wsdl.url"/> </not>
diff --git a/org.bridgedb.tools.qc/build.xml b/org.bridgedb.tools.qc/build.xml
index ca9d6119a..da6bd32eb 100644
--- a/org.bridgedb.tools.qc/build.xml
+++ b/org.bridgedb.tools.qc/build.xml
@@ -1,9 +1,11 @@
 <?xml version="1.0"?>
 <project name="org.bridgedb.tools.qc" default="dist" basedir=".">
   
+	<import file="../build-common.xml" />
+
 	<!-- absolute deps are used for building, testing and in the manifest classpath -->
 	<path id="absolute.deps">
-		<fileset dir="../dist">
+		<fileset dir="${bundle.dest}">
 			<include name="org.bridgedb.jar"/>
 			<include name="org.bridgedb.bio.jar"/>
 			<include name="org.bridgedb.rdb.jar"/>
@@ -35,6 +37,4 @@
 	</jar>
   </target>
 
-	<import file="../build-common.xml" />
-
 </project>
diff --git a/org.bridgedb.webservice.biomart/build.xml b/org.bridgedb.webservice.biomart/build.xml
index 44f2b3300..0bf8d67d4 100644
--- a/org.bridgedb.webservice.biomart/build.xml
+++ b/org.bridgedb.webservice.biomart/build.xml
@@ -1,5 +1,7 @@
 <?xml version="1.0"?>
 <project name="org.bridgedb.webservice.biomart" default="dist" basedir=".">
+
+	<import file="../build-common.xml" />
 	
 	<path id="absolute.deps">
 		<pathelement location="../dist/org.bridgedb.jar"/>
@@ -28,6 +30,4 @@
 			todir="build/org/bridgedb/webservice/biomart/util" />
 	</target>
 
-	<import file="../build-common.xml" />
-
 </project>
diff --git a/org.bridgedb.webservice.bridgerest/build.xml b/org.bridgedb.webservice.bridgerest/build.xml
index c221a37a0..a1e4740aa 100644
--- a/org.bridgedb.webservice.bridgerest/build.xml
+++ b/org.bridgedb.webservice.bridgerest/build.xml
@@ -1,5 +1,7 @@
 <?xml version="1.0"?>
 <project name="org.bridgedb.webservice.bridgerest" default="dist" basedir=".">
+
+	<import file="../build-common.xml" />
 	
 	<path id="absolute.deps">
 		<pathelement location="../dist/org.bridgedb.jar"/>
@@ -20,6 +22,4 @@
 	<path id="test.deps">
 	</path>
 
-	<import file="../build-common.xml" />
-
 </project>
diff --git a/org.bridgedb.webservice.cronos/build.xml b/org.bridgedb.webservice.cronos/build.xml
index 37928c1fd..da4f11cb9 100644
--- a/org.bridgedb.webservice.cronos/build.xml
+++ b/org.bridgedb.webservice.cronos/build.xml
@@ -1,6 +1,8 @@
 <?xml version="1.0"?>
 <project name="org.bridgedb.webservice.cronos" default="dist" basedir=".">
 
+	<import file="../build-common.xml" />
+
 	<!-- absolute deps are used for building, testing and in the manifest classpath -->
 	<path id="absolute.deps">
 		<fileset dir="../dist">
@@ -25,9 +27,7 @@
 		<pathelement location="../org.bridgedb/build-lib/measure.jar"/>
 	</path>
 
-	<import file="../build-common.xml" />
-
-	<target name="build" depends="prepare, prepare-common, prepare-jar-name">
+	<target name="build" depends="prepare, prepare-common">
 		<javac srcdir="src-axis"
 			   includes="**"
 			   debug="true"
diff --git a/org.bridgedb.webservice.picr/build.xml b/org.bridgedb.webservice.picr/build.xml
index ef7191e2b..09e7f47e6 100644
--- a/org.bridgedb.webservice.picr/build.xml
+++ b/org.bridgedb.webservice.picr/build.xml
@@ -1,6 +1,8 @@
 <?xml version="1.0"?>
 <project name="org.bridgedb.webservice.picr" default="dist" basedir=".">
 
+	<import file="../build-common.xml" />
+
 	<!-- absolute deps are used for building, testing and in the manifest classpath -->
 	<path id="absolute.deps">
 		<fileset dir="lib">
@@ -26,6 +28,4 @@
 		<pathelement location="../org.bridgedb/build-lib/junit4.jar"/>
 	</path>
 
-	<import file="../build-common.xml" />
-
 </project>
diff --git a/org.bridgedb.webservice.synergizer/build.xml b/org.bridgedb.webservice.synergizer/build.xml
index bbc2b2f8d..5d4398804 100644
--- a/org.bridgedb.webservice.synergizer/build.xml
+++ b/org.bridgedb.webservice.synergizer/build.xml
@@ -1,12 +1,14 @@
 <?xml version="1.0"?>
 <project name="org.bridgedb.webservice.synergizer" default="dist" basedir=".">
 
+  <import file="../build-common.xml" />
+
 	<!-- absolute deps are used for building, testing and in the manifest classpath -->
 	<path id="absolute.deps">
 		<fileset dir="lib">
 			<include name="*.jar"/>
 		</fileset>
-		<fileset dir="../dist">
+		<fileset dir="${bundle.dest}">
 			<include name="org.bridgedb.jar"/>
 			<include name="org.bridgedb.bio.jar"/>
 		</fileset>
@@ -29,6 +31,4 @@
 		<pathelement location="../org.bridgedb.rdb/lib/derby.jar"/>
 	</path>
 
-  <import file="../build-common.xml" />
-
 </project>
diff --git a/org.bridgedb.webservice.uniprot/build.xml b/org.bridgedb.webservice.uniprot/build.xml
index 63350d7b3..36fc440ee 100644
--- a/org.bridgedb.webservice.uniprot/build.xml
+++ b/org.bridgedb.webservice.uniprot/build.xml
@@ -1,9 +1,11 @@
 <?xml version="1.0"?>
 <project name="org.bridgedb.webservice.uniprot" default="dist" basedir=".">
+
+	<import file="../build-common.xml" />
 	
 	<!-- absolute deps are used for building, testing and in the manifest classpath -->
 	<path id="absolute.deps">
-		<fileset dir="../dist">
+		<fileset dir="${bundle.dest}">
 			<include name="org.bridgedb.jar"/>
 			<include name="org.bridgedb.bio.jar"/>
 		</fileset>
@@ -26,6 +28,4 @@
 		<pathelement location="../org.bridgedb/build-lib/junit4.jar"/>
 	</path>
 
-	<import file="../build-common.xml" />
-
 </project>
diff --git a/org.bridgedb/build.xml b/org.bridgedb/build.xml
index 0d8718155..d22644844 100644
--- a/org.bridgedb/build.xml
+++ b/org.bridgedb/build.xml
@@ -1,6 +1,8 @@
 <?xml version="1.0"?>
 <project name="org.bridgedb" default="dist" basedir=".">
-	
+		
+	<import file="../build-common.xml" />
+
   <property name="svn.exec.svnversion" value="svnversion"/>
   
   <property file="version.props"/>
@@ -25,7 +27,7 @@
 
 	<target name="prepare">
 		<tstamp /> <!-- set ${TODAY} and ${TSTAMP} -->
-		<mkdir dir="../dist"/>
+		<mkdir dir="${bundle.dest}"/>
 		<exec executable="${svn.exec.svnversion}" outputproperty="subversion_revision" failifexecutionfails="false">
 			<arg line="-n ."/>
 		</exec>
@@ -37,7 +39,5 @@ COMPILE_DATE=${DSTAMP} ${TSTAMP}
 bridgedb.version=${bridgedb.version}
 		</echo>  
 	</target>
-		
-	<import file="../build-common.xml" />
 
 </project>