Cleanup and harmonize output streams

We currently have several instances for std::cout and std::cerr throughout the code. We now have a Logger that we can use instead.

• We can replace most std::cerr instances with Log::error() (or Log::warning() depending on the severity)
• We can replace most std::cout with Log::misc().
• We currently have some commented out std::cout for debugging. Assess whether they are still needed and either remove or replace with Log::misc().

We may want to consider supporting both std::cout and std::cerr by default in the logger, but I personally don't think that's necessary.

Note: in earlier profiling, Log::misc() << "some output" << std::endl; would show up as a hotspot. I recommend "\n" moving forward unless flushing is really necessary.

CC @PhilipFackler @pelesh