Indices - basedata_ref should be an argument, not an object parameter

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The calculations system currently requires that a basedata ref is set in all 
cases.  

It would be more generic if basedata_ref were set as a required arg for those 
subs which need it.  Currently this is nearly all of them, but putting the 
basedata at the same level as trees and matrices will allow broader usage (e.g. 
analyses using only trees).  

Original issue reported on code.google.com by shawnlaffan on 6 Oct 2014 at 6:45