(In reply to comment #0)
> If you specify the full path on node for stagein file, everything will be
> deleted
> in the specified folder including the folder itself.
> For example (Warning! first backup /home/user folder on node1)
> 
> $pwd
> /home/john
> $touch input.txt
> $echo "sleep 10" | qsub -l nodes=1,walltime=100 -W
> stagein=/home/user/input.txt@node1:/home/john/input.txt
> 
> After the job completed everything in /home/user folder including (/.ssh/
> .bashrc, etc) are deleted on node1

Sorry for my poor english. To be more specific the nodes parameter could be
determined.
$echo "sleep 10" | qsub -l nodes=node1,walltime=100 -W
stagein=/home/user/input.txt@node1:/home/john/input.txt

The stagein parameter without the full path works as expected.
$echo "sleep 10" | qsub -l nodes=node1,walltime=100 -W
stagein=input.txt@node1:/home/john/input.txt
Only the input.txt are deleted on node1.

This has been fixed in 2.5, 3.0, etc.