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

Conflicts:
	DESCRIPTION
	R/createMassBank.R
	R/leMsmsRaw.R

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

Refactoring: aggregation, recalibration. Also in theory done, but still untested: step 5 (analysis 2)  and 6 (reaggregation); and completely unfinished: reanalysis and multiplicity filtering

Fixes in the workspace update function to reflect behaviour of the pre-refactoring version during aggregation
Methods for selection from aggregate table and for spectra filtering

Merge branch 'master' into refactoring and subsequent edits - merged master developments forward to refactored branch

Merge for BioConductor release

Please pull the christmas fixes we just discussed on the phone with Emma