Added annotations
Added fas library in BuildFile.xml
Removed layer merging in StubCleaner

- used min dZ instead of dEta, a cut on dZ < 26 cm is applied to get rid of loopers
- kept stubs with trkId == -1 that fail to find a matched simTrack
- dropped TTStubs_iModCols and TTStubs_iModRows
- updated testStubCleaning.py
Added SuperstripStitcher to stitch a pattern of superstrips

- Used separate variable size for barrel and endcap superstrips in SuperstripArbiter. Updated PatternBankOption and amsim correspondingly
- Corrected hashing for fake superstrips in SuperstripHasher
- Implemented tests in TestSuperstripOperations
- Fixed bugs in AMSimulationDataFormats/Helper.h
Minor improvements in StubCleaner, TrackFitter, NTupleMaker
Added default values for variable superstrip size
Moved pattern_type typedef from TTPattern.h to Helper.h

- Disabled dictionary generation
- Added etaFromTheta() and etaFromRhoZ() in HelperMath.h
- Also updated AMSimulationLinkDef.h
Modified to use pattern_type in SuperstripStitcher
Completely flensed PatternGenerator

- Currently uses simple std::map operation
  - fas integration still pending
- Modified to do variable superstrip size and n-choose-k combinations
- Completely removed DC bits
- Dropped TTPattern
- Read trigger towers from PatternBankOption
- Updated testPatternBankGeneration
Massive clean up of TTPattern, TTSuperstrip

- TTPattern and TTSuperstrip are no longer used.
Completely flensed PatternMatcher

- Currently uses simple std::vector operation
  - fas integration still pending
- Modified to do variable superstrip size and collision-free hashing
- Completely removed DC bits
- Updated testPatternRecognition
- Removed testEncoding
Sped up reading in PatternGenerator

- Minor improvements in other codes
Enabled timing printout in tests.
Minor optimizations in SuperstripArbiter, SuperstripHasher, SuperstripStitcher

- Improved exception handling
Minor optimizations in StubCleaner, PatternGenerator, PatternMatcher, NTupleMaker

- Included coverage printout in PatternGenerator
- Kept genParticle charge in PatternMatcher
- Dropped trkVertices_* and simVertices_* in NTupleMaker
Changed to file buffer for writing in PatternMatcher and TrackFitter

- Added minFrequency option in PatternMatcher
Changes in batch scripts
Added skeleton for amconvert
Changed count_type to 16-bit to avoid integer overflow
Merge pull request #13 from jiafulow/prepare-v020

Restructured the entire codebase