RF: use sequences for run_command script tester

`run_command` was using strings rather than sequences passing in the
``Popen`` constructor.  This blows up when there are space in the passed
paths.  Use the sequence command definition instead.
RF: put pwd on path running tests from dipy dir

Some of the script tests change directory before running the scripts.
These will fail if the dipy we picked up is in the current working
directory (running from the dipy root directory). Check for this case
and put the directory on the path before running the scripts.