I am trying to find the configuration.yaml file that is used when I use the online gui to add and remove integrations. I do a mixture of manual config and GUI config and I would just like to have a backup of both. Is it in the hass_config folder somewhere?
The integrations added via gui are not stored in a yaml file. They are stored in json files under $CONFIG/.storage where $CONFIG depends how you installed home assistant.
Hassio it is /config
gotcha, so if I reset my docker container it should automatically pick that json up and continue working?
Yes, when you run ha in docker the entire /config directory is stored on the ‘host’, not in the container. That is what the -v option does 
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