Add logfile kwarg to staging area runcmd

We use tee to write the output to a file as well as to stdout.
Using Popen it should be straight forward to send the output to a pipe and
then read that pipe and write to wherever.
At the moment morph uses cliapp's runcmd rather than Popen. cliapp's runcmd
is a blocking call, so we're not able to read from the pipe until the
command has completed, which prevents real time logging to a number of files.
One solution to this problem might be to spawn a thread which opens a pipe
to the command being executed, the thread then reads from the pipe and writes
to our collection of logfiles.

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