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