support for PBS Pro thanks to Davide Rambaldi
Fixes for PBS Pro executor from Davide
fix complex pipelines starting with list failing with bouncer errors
Merge branch 'master' of https://code.google.com/p/bpipe
fix R aborting when user hits control-c in some situations
fix branch variables not accepted as required parameters
fix output does not include branch if no input as base and output extension syntax used
fix test giving fail status even though it passes
minor comment changes
Make failure to clean up files much more obvious and add reattempt on shutdown - followup from analysis of some cases where files did not get cleaned up
Fix second and later outputs possibly not cleaned up in some situations of command failure
test for cleaning up 2nd and later outputs
merge googlecode