Recover the same behavior of PatternGenerator with --no-filter

Minor bug fixes in amsim_crab.cfg and amsim_crab.sh
Changes in the plotter tools
Changed muon eta from [-3,3] to [-2.5,2.5]
Set more branches in PatternGenerator.cc and PatternMatcher.cc
Changed the logic of stub filtering
Changed layer map used for layer merging
Re-implemented fake superstrip workflow
Changes in the plotter tools. [2]
Merge pull request #3 from jiafulow/prepare-v011

Changed stub filtering and fake superstrip implementations