clj-kondo was updated to support the newest linting tools in deps.edn in clojure CLI 1.10.3.933. it's released in 2021.08.03.

The lastest tools-deps seems have different way on calculate paths?

@doglooksgood Different to... some other tool? Do you mean classpath or some other paths?

My project has a setup to start shadow-cljs with a few aliases. like [:dev :test :cljs :cljs-test]. In :test alias I have a :extra-paths which add "test/clj" . After upgraded to latest version of tools-deps, test/clj is not collected in CLASSPATH, but it should be. If I move the :extra-paths from :test to :dev the CLASSPATH is correct. Since there are few tools cider, shadow and tools-deps. I'm not sure where the problem comes from.

when CIDER starts up at the top of the repl it should print the startup command. You can copy that and then continue your investigations from a repl to do exactly what CIDER is doing for you, and then eliminate CIDER's middleware and other things to see if CIDER is the culprit. If not, you have removed one extra player and can continue investigating

@dpsutton good idea, I'll have a try

you can also work from the other side. just start up your project with the aliases you want and assert that your classpath has whatever entry you want. if it doesn't work with all tooling removed it just won't work at all