Default output padding

[shuds13]

Should we add a default padding to output sim dir numbers?
e.g.

ensemble/
  sim00001/
  sim00002/

instead of the current

ensemble/
  sim1/
  sim2/

Either way, there will be an option to give a padding width, and overflow will just add digits as needed.

[shuds13]

Feel free to ask questions on this here.