With the helpful advice from people who have answered here I started digging into One-Jar. After some dead-ends (and some results that were exactly like my previous results I managed to get it working. For other peoples reference I'm listing the build.xml that worked for me.
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<project basedir="." default="build" name="<INSERT_PROJECT_NAME_HERE>">
<property environment="env"/>
<property name="debuglevel" value="source,lines,vars"/>
<property name="target" value="1.6"/>
<property name="source" value="1.6"/>
<property name="one-jar.dist.dir" value="../onejar"/>
<import file="${one-jar.dist.dir}/one-jar-ant-task.xml" optional="true" />
<property name="src.dir" value="src"/>
<property name="bin.dir" value="bin"/>
<property name="build.dir" value="build"/>
<property name="classes.dir" value="${build.dir}/classes"/>
<property name="jar.target.dir" value="${build.dir}/jars"/>
<property name="external.lib.dir" value="../jars"/>
<property name="final.jar" value="${bin.dir}/<INSERT_NAME_OF_FINAL_JAR_HERE>"/>
<property name="main.class" value="<INSERT_MAIN_CLASS_HERE>"/>
<path id="project.classpath">
<fileset dir="${external.lib.dir}">
<include name="*.jar"/>
</fileset>
</path>
<target name="init">
<mkdir dir="${bin.dir}"/>
<mkdir dir="${build.dir}"/>
<mkdir dir="${classes.dir}"/>
<mkdir dir="${jar.target.dir}"/>
<copy includeemptydirs="false" todir="${classes.dir}">
<fileset dir="${src.dir}">
<exclude name="**/*.launch"/>
<exclude name="**/*.java"/>
</fileset>
</copy>
</target>
<target name="clean">
<delete dir="${build.dir}"/>
<delete dir="${bin.dir}"/>
</target>
<target name="cleanall" depends="clean"/>
<target name="build" depends="init">
<echo message="${ant.project.name}: ${ant.file}"/>
<javac debug="true" debuglevel="${debuglevel}" destdir="${classes.dir}" source="${source}" target="${target}">
<src path="${src.dir}"/>
<classpath refid="project.classpath"/>
</javac>
</target>
<target name="build-jar" depends="build">
<delete file="${final.jar}" />
<one-jar destfile="${final.jar}" onejarmainclass="${main.class}">
<main>
<fileset dir="${classes.dir}"/>
</main>
<lib>
<fileset dir="${external.lib.dir}" />
</lib>
</one-jar>
</target>
</project>
I hope someone else can benefit from this.