Implement logging in manipulate subpackage

Now, the logging module is used to convey messages to the user.
Basically, print(x) was replaced with LOG.(error|warn|info)(x) as
appropriate. You should call ts.manipulate.setup_console_logging() at
the start of any scripts if you want verbose logging.

 Changes to be committed:
	modified:   timestream/manipulate/__init__.py
	modified:   timestream/manipulate/correct_detect.py
	modified:   timestream/manipulate/pipecomponents.py
KDM review of whole mainipulate subpackage

FIXME comments added, logging set up, flake8 errors largely fixed, some
major refactoring still to do.

 Changes to be committed:
	modified:   timestream/manipulate/configuration.py
	modified:   timestream/manipulate/correct_detect.py
	modified:   timestream/manipulate/netcdf.py
	modified:   timestream/manipulate/pipecomponents.py