Up until recently I was running some 1.40x build with subversion plugin 1.23 (ubuntu 10.04 w/ tomcat 6), but then I upgraded to 1.447 w/ subversion plugin 1.37.

While cleaning workspaces, it was now trying to delete stuff inside directories symlinked in the workspace, i.e.:

Started by user anonymous
Building on master
Cleaning local Directory working/checkout
java.io.IOException: Unable to delete /usr/share/tomcat/.hudson/jobs/navl-official-single-plugin-build-2.7.0/workspace/working/checkout/platform/tools/amd64-chroot/home/tomcat6
at hudson.Util.deleteFile(Util.java:263)

where "working" there is actually a symlink to a dir outside of /usr/share/tomcat.

I first downgraded back to 1.401, and even after restarting tomcat it was still trying to follow symlinks during cleanup. Then I downgraded the subversion plugin to 1.23, and it started working as before.