Update 2 for anyone else with that timeout: that particular technique for persisting files did not work in Codefresh, but the principle does work.
Since YAML is a superset of JSON, I figured that the config file could be JSON. Despite the CLI looking for a config.yml file. And so I turned my config.yml into JSON so I could then store it in a secret (maybe I could do that directly with a YAML file, but figured the whitespace may cause fails if stored as a string). And then in CI, simply wrote that secret into a /config.yml prior to running fly deploy. Then … no waiting, and no time-outs. And builds now take seconds rather than many minutes (with all the time-outs, fails and fist-shaking too).
Yay. 