When I plan a workflow using 4.0.0, and my site has an environment variable of PEGASUS_HOME=/usr/local/pegasus/foo, when I plan the workflow using shared file system mode and condor style, I get a create dir job and a stage in job that both use executables in "/usr/local/pegasus-4.0.0/foo/bin". This incorrect path is used for pegasus-kickstart, pegasus-create-dir, pegasus-transfer.

On my local machine I have "/usr/local/pegasus" as a symlink to "/usr/local/pegasus-4.0.0". When I change my actual directory to "/usr/local/pegasus-foo" and update the symlink, the incorrect path in the submit files becomes "/usr/local/pegasus-foo/foo/bin".

It appears that somewhere Pegasus is treating a remote path as if it is local and, finding the same local path, is resolving the symlinks in that path locally.