Running the build from my home directory like so:
ant -lib projectEndings/diagnostics/utilities -f projectEndings/diagnostics/build.xml -DprojectDir=ise/ise3/svn/data/
Results in the build looking for this directory:
Output dir: /home/netlink/jtakeda/projectEndings/diagnostics/ise/ise3/svn/data/
So it looks for ${base.dir}/{$projectDir}--should it be ${user.dir}/${projectDir}?