Allow rose-stem to read a variable from the rose.conf file

Attempt to look into #1315, which is supposed to allow rose-stem to read a 'site' variable from the rose.conf file to allow the value to be defined once per site, rather than by every user on the command line every time they run rose-stem.

@matthewrmshin, when you get chance would you mind reviewing this please? (if you can think of a better way of doing it I'm happy to go with it)
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