If you move to an ANT (or Maven, for you Maven fans) then you can automate the Jar building very nicely, and also use it outside of Eclipse (e.g., in an automated build environment). All you need to do is copy the files from your src, jsp, foobar and resources locations into a build staging folder, then Jar the resulting files using ANT's Jar task.
<target name="makejar" depends="compile, copyfiles">
<jar destfile="${jars.dir}/myjarfile.jar" index="true" basedir="${build.dir}" />
</target>
One thing I look down on is including non-source (except package.html files for Javadoc) within the src folder. If you feel you have to do this to achieve something, then you are doing it wrong.