Allow for customizable config directory.

Update settings.py.dist to not use settings any path helpers, just normal
strings for paths.

refs #16269
Add default values of config opts in config docs

refs #16269
configuration docs: Add info about SECRET_KEY and WEB_MGR_API_KEY

refs #16269
Update more docs pages to refer to config.yml

Also update configuration docs to refer to other doc pages for more info.

Remove old ssh-keys-example, there is a newer example in the utils folder.

refs #16269