Feature 414 part1: removed machineid as mandatory argument for submit_job and list_jobs

General comments
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* As foundation of removing machineid as mandatory argument in TMS command, the EMF model has been updated
* This first PR also removes the requirement on machineId in submit_job and list_jobs.
* In submit job, if no machine is specified, 'autom' is used
  * you can specify a target machine using the option --machineId or -r (shortoption)
* In list job, if no machine  is specified, 'all' is used
  * you can specify a target machine using the option --machineId or -m (shortoption)
* There are also some misc refactoring and variable renaming