list of substitutions variables @FOO@ is not consistent among commands or options

[Roland Haas]

Simfactory does not use a consistent list of replacement variables for all substitutions. There are differences between runscripts and submitscripts, some of which are justified, eg the job id is not yet available by the time the submit script is created. Some are not justified, for example the machine ini files replace @USER@ in the basedir setting but not in optionlist settings.

Ideally these should be handled consistently using a single replacement function.