Fix ChiselStage and Builder handling of logging (#3895)

Previously, object circt.stage.ChiselStage was ignoring the Logger.
Also, Chisel was not creating its own logger scope which could lead to
clobbering of the Console when running invoking Chisel in the same
process multiple times.

Fix various places we had to workaround this behavior and fix tests
checking --log-level debug.

(cherry picked from commit 88d147d9)

# Conflicts:
#	core/src/main/scala/chisel3/experimental/hierarchy/core/Definition.scala
#	core/src/main/scala/chisel3/internal/Builder.scala
#	docs/src/cookbooks/cookbook.md
#	src/main/scala/chisel3/aop/injecting/InjectingAspect.scala
#	src/main/scala/chisel3/stage/phases/Elaborate.scala
#	src/main/scala/circt/stage/ChiselStage.scala
#	src/test/scala/circtTests/stage/ChiselStageSpec.scala