Move phase business out of plugin

src/main/scala/leon/Analysis.scala

src/main/scala/leon/ArrayTransformation.scala

src/main/scala/leon/EpsilonElimination.scala

src/main/scala/leon/FunctionClosure.scala

src/main/scala/leon/FunctionHoisting.scala

src/main/scala/leon/ImperativeCodeElimination.scala

src/main/scala/leon/LeonContext.scala

src/main/scala/leon/LeonPhase.scala

src/main/scala/leon/Simplificator.scala

src/main/scala/leon/TypeChecking.scala

src/main/scala/leon/UnitElimination.scala

src/main/scala/leon/synthesis/SynthesisPhase.scala