Added stageout to run command.

Added
=====

* The run command now calls stageout before exiting.
* Write a README file in a run directory before stagin and stageout.

Changed
=======

* Changed 'input_files' attribute of a component to just 'files', which
  matches the name of its corresponding JSON file.
* Hooks are now run in the run directory for that component. No need for
  the hook to change to that directory itself.
Merge branch 'master' of https://github.com/csdms/wmt