Revamped SuperstripStitcher class

Updated tests following the changes
Merged SuperstripArbiter and SuperstripHasher classes

Removed SuperstripHasher subsequently
Incorporated lean_merger3 class
Implemented trigger tower logic
Other updates following the changes
Defragment AMSimulationDataFormats and program options

More cleanup in SuperstripArbiter and SuperstripStitcher classes
Cleaned up following defragmentation

Make the stubs sorted according to moduleId in StubCleaner
Implemented removal of patterns not contained within a trigger tower in PatternGenerator
Propagated changes to mock algorithms
Merge pull request #15 from jiafulow/prepare-v022

Revamped SuperstripStitcher and SuperstripArbiter