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Since 0.16.0, the container filter defaults are applied only to the config built from command line options. With -config, stopped containers are included, and onlyexposed (used in the README and in examples/docker-gen.cfg), onlypublished and includestopped are silently ignored. Templates then see stopped containers without networks, which can, for example, produce empty nginx upstreams.
This restores the three config file options and applies the same defaults to every config. It also documents config.ContainerFilter for config files, and fixes the filter names in the -only-exposed and -only-published help (expose and publish).