Not cider, but I use envrc and direnv for that

This: https://github.com/purcell/envrc?

Yes, that project also popped up in this recent discussion https://clojurians.slack.com/archives/C099W16KZ/p1701028228710109 Generally, for JVM processes consider favoring setting Java propeties (controllable with tools.deps aliases / Lein profiles) over env variables - they're more idiomatic and flexible (can be changed at runtime)

How would I set a JVM property in Cider/clojure-lsp then?

you set it with :jvm-opts in a specific deps.edn alias and tell cider to use that alias

Does that instruction get bundled with the jar if you run uberjar?

uberjars are run with java , so you run approximately java myuber.jar -Dmy.property=123