Process SystemCommand arguments in list format

Previously, SystemCommand commands and arguments were processed as
strings which caused problems during shell interpretation if the
arguments were not escaped properly.  Now all commands are expressed
as arrays and no longer require their arguments to be escaped.
Additionally, stderr and stdout could have been interleaved in the
past and now they are always separated.
Merge pull request #2624 from vmrob/system-command

Process SystemCommand arguments in list format