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Update logging strategy

Closes #4.
- the log file handler always records to DATA_DIR/log, and creates the
directory when being set up (this requires some patching in the tests to
avoid that the system outside the tests is modified)
- documentation updates
- the log file handler is now always set up before the Flask app is
created. This enables having as much information logged persistently as
possible, and hence improves debugging when the Flask app is not
attached to a terminal at start

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