Changed it so that molfiles don't get generated when tentative or unknown, also no mention in list.tsv

Fixed issues that arose in current R-devel (3.3), which apparently introduced a behaviour change in aggregate() and makes rcdk generate.formula() produce warnings.

Several changes, refactoring almost complete, showmethod adjusted, much less notesand warnings in R CMD check, isotopic annotation error fixed

Updated inline documentation for new arguments and new classes/methods. Fixed minor bugs. Passes R CMD check w/ standard vignette.

Completed workspace update loading; fixes in workflow for cleanly rerunning all steps and for copying recalibration