Merge branch 'master' into updatedeprecations

# Conflicts:
#	src/main/scala/firrtl/annotations/JsonProtocol.scala
#	src/main/scala/firrtl/transforms/Dedup.scala
#	src/test/scala/firrtlTests/FirrtlSpec.scala
#	src/test/scala/firrtlTests/FlattenTests.scala
#	src/test/scala/firrtlTests/InlineInstancesTests.scala
#	src/test/scala/firrtlTests/PassTests.scala
#	src/test/scala/firrtlTests/transforms/TopWiringTest.scala