Renamed directories:

AliBase -> Base
AliData -> Data
AliGenerators -> Generators

Namespace changes for classes:

O2Detector -> Detector
O2Module -> Module
O2TrackReference -> TrackReference
AliDetectorList -> DetectorList
AliStack -> Stack
AliMCTrack -> MCTrack

Correctly set ClassImp to namespaces

Removed namespace prefixes from the UpgradeV1Layer class

Renamed LinkDefs and library names to conform to the coding guidelines