I wrote a quick sample app that demonstrates the issue. Inside its Meteor.startup method, I have
console.log(process.env.MONGO_URL);
when this runs I see the following (as a single line) in the log
mongodb://USER:PASSWORD@mongo1:27017,mongo2:27017,mongo3:27017/DB?replicaSet=RS&readPreference=primaryPreferred&w=majority&autoReconnect=true&ssl=true
At that point we are past all shell manipulation, etc.
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Kept digging… Leaving this here just in case anyone else runs into a similar wall in the future.
There is some difference between how k8s pulls in env variables using envFrom.secretRef and from env with a secretKeyRef value. Even though everything looks good.
Not sure what the difference is, but switching to the latter made everything work.