I just turned on symlinks for a workflow and ended up with a in file like:

#local
symlink:///runs/galactic-plane/firefly/galactic-plane-20101109_133012/00001.params
#local
file:///runs/galactic-plane/firefly/galactic-plane-20101109_133012/outputs/rynge/pegasus/gp/20101109T133012-0800/00001.params

pegasus-transfer expects symlinks to show up as file://->symlink:// and hence the in file should have been:

#local
file:///runs/galactic-plane/firefly/galactic-plane-20101109_133012/00001.params
#local
symlink:///runs/galactic-plane/firefly/galactic-plane-20101109_133012/outputs/rynge/pegasus/gp/20101109T133012-0800/00001.params

(note that the paths are in the right order, they are just prefixed wrong)