Improve logging across the library

[dokempf]

#327 added logging support to the library.

There are numerous ways to improve logging across the library:

• Turn existing warnings into logger.warn
• Write logger.info messages where ever a user might be interested in progress that is happening
• Write logger.debug informations where developers might be interested in what is happening
• Equip more apps with a logging output widget, see pipeline_tuning for how it is done

[dokempf]

This should be an ongoing effort going into the future.