I do have a .clj-kondo dir and clj-kondo has managed to put other configs there.

Can you check if the dependency contains those files?

you can e.g. do this with ls_jar: https://github.com/borkdude/tools#ls_jar

or jar -tf

% zipinfo ~/.m2/repository/lilactown/helix/0.1.7/helix-0.1.7.jar| grep kondo
-rw----     2.0 fat        0 bl defN 22-Mar-29 21:15 clj-kondo.exports/
-rw----     2.0 fat        0 bl defN 22-Mar-29 21:15 clj-kondo.exports/lilactown/
-rw----     2.0 fat        0 bl defN 22-Jul-29 17:12 clj-kondo.exports/lilactown/helix/
-rw----     2.0 fat    10661 bl defN 22-Jul-29 17:12 clj-kondo.exports/lilactown/helix/config.edn
-rw----     2.0 fat        0 bl defN 22-May-12 20:52 clj-kondo.exports/lilactown/helix/clj_kondo/
-rw----     2.0 fat        0 bl defN 22-Aug-11 17:28 clj-kondo.exports/lilactown/helix/clj_kondo/lilactown/
-rw----     2.0 fat     3566 bl defN 22-Aug-11 17:28 clj-kondo.exports/lilactown/helix/clj_kondo/lilactown/helix.clj

that looks ok

I even tried adding the helix-dep to my main :deps, but it didn't help. Previously it was only under my :shadow-cljs alias.

you need to add --lint $(clojure -Spath)

did you have that? this wasn't clear from your OP

now it worked

% clj -M:clj-kondo --dependencies --copy-configs --lint $(clojure -Spath)
Configs copied:
- .clj-kondo/com.github.seancorfield/next.jdbc
- .clj-kondo/lilactown/helix
- .clj-kondo/metosin/malli

I thought --dependencies --copy-configs would do the right thing on its own. I guess I should reread the docs.

thanks!

ah yes, you always need to specify the classpath to clj-kondo explicitly, there is absolutely no magic with deps.edn detection etc :)

I get it now, yeah, kondo doesn't read my deps.edn

That makes perfect sense