Refactored isobar import (readIBSpectra, merge identifications, etc)

Merging of identifications has been reimplemented (it even seemed it
would not have worked before, anymore), and basic MSGF+ import functions
have been added.
use ldply in estimateRatioForPeptide instead of t(sapply(...)), which always returns a data.frame
Fix substring of worksheet name (from first instead of second position)
improved MSGF+ imprt
correctly call new("IBSpectra",...) with identifications argument instead of data
added 'aa.before' and 'aa.after' columns
updated documentation
small fixes