Updating readme with lems paper info

Updating version num to 0.9.5.3, for the nml2 beta 3 release, to
distinguish it from past development version
Updates to error messgaes & some extra @Override in StateInstance.java
Updating lems windows starter
Adding MIT license
Merge branch 'master' into test_gap_junctions

Conflicts:
	lems
	lems.bat
	pom.xml
	src/main/java/org/lemsml/jlems/core/run/StateInstance.java
	src/main/java/org/lemsml/jlems/io/Main.java