Fix ChiselStage and Builder handling of logging (backport #3895) (#3898)

* 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:
#	src/main/scala/circt/stage/ChiselStage.scala

* Resolve backport conflicts

* Make logger annotations unserializable

Change logger annotations to mix-in the Unserializable trait so that they
will not emitted by a stage.  These annotations are not intended to be
seen by CIRCT and these should be stripped from the output FIRRTL text.

Signed-off-by: Schuyler Eldridge <schuyler.eldridge@sifive.com>

---------

Signed-off-by: Schuyler Eldridge <schuyler.eldridge@sifive.com>
Co-authored-by: Jack Koenig <koenig@sifive.com>
Co-authored-by: Schuyler Eldridge <schuyler.eldridge@sifive.com>