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
Created a Doxygen configuration file, to create the documentation execute doxygen AliceO2Doxygen.conf

Edited the markdown file to also conform with the doxygen markdown format