Added hitEvtIds for clusters and stubs, local coordinates for stubs
Added maxPatterns option in PatternMatcher
Separated classes and functions from drawer_pgun.py

Used more events for pattern generation
Added img000.root..img004.root
Various minor fixes in NTupleTools
Added pixelDigi info
Minor fixes
Updated batch scripts
Changed the tower indexing in PatternGenerator
Changes in the plotter tools

- Added drawer_layerdisk.py
Changes in the plotter tools. [2]

	renamed:    drawer_bankgen.py -> drawer_amsim.py
Changes in the plotter tools. [3]

- Reduce LOC of drawer_layerdisk.py
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
Merge pull request #4 from jiafulow/prepare-v012

Added PixelDigi info, added StubCleaner class, and created AMSimulationDataFormats subpackage