Merge pull request #5 from goullet/BooleanSwitchingAnnotations

Boolean switching annotations
added new realizability code
updated install-mac.sh
extra quote mark in install-mac.sh
Updates for Boost 1.56 and new homebrew web address
inequality constraints
removed debug code that accidentally made it into master
New feature to pin down factors in Boolean Switching
Changed Atlas indexing, implemented C++11 loops here and there
modification for bree
Merge branch 'master' of https://github.com/sharker81/conley-morse-database into BooleanSwitchingAnnotations