Plugin creation use cases

##Plug and play Take a simple tool that is used on the command line and put it to use in copernicus. Should test the default behaviour of an individual function and functions that are connected together.

Suggested command line tools for this case : grompp, grep

##Plug and extend A command line tool where we need to override the default behaviour

Suggested command line tools for this case : mdrun, MSMbuilder Other suggestions : graph algorithm

##Repeated run programs that need checkpointing. Should be greatly simplified and job resubmission logic should be handled automatically by copernicus

Suggested command line tools for this case : mdrun, another simulation package?