Created AMSimulationDataFormats subpackage

- Removed hash completely
Moved makeLayerMap() function
Added StubCleaner class

- Added testStubCleaning.py
Removed filterHits() from PatternGenerator

- Fixed tests for PatternGenerator
Added tcut2.C and runTheMatrix.csh
Changes in NTupleTools to run on official samples that dropped simSiPixelDigis and BeamSpotFromSim