Merge branch 'devel'

Conflicts:
	R/ProteinGroup-class.R
Merge branch 'devel'
Merge branch 'devel'
Merge branch 'devel'
Merge branch 'devel'
Merge branch 'devel'
Merge branch 'devel'
Merge branch 'devel'
Merge branch 'devel'
Merge branch 'devel'
Merge branch 'devel'
Merge branch 'ptm'
Merge branch 'ptm'
Merge branch 'ptm'
Merge branch 'devel'
improved MSGF+ import
improved MSGF+ import
replaced $ access to report environments with [[]]
added function readProteinGroup2 which merges identifications
cleaned up id file import