Specify the stage for command-line driver

Currently workflow driver for offline FOM does not need to specify the stage to run. While the intention was to reduce the job-scripting effort, it can make the job script unclear about what stage is being run.

In future the command-line driver should take the stage as an input argument. Certain stages need to read a restart file, and when a restart file is read, the stage saved in the restart file must be consistent with the stage in the input argument.