Is it because the file name uses a - rather than _

no, that's a poor choice of example on my part I suppose, the file is named api.clj

If I pass in the directory I want as my :src-dir the outputted classes directory contains a file named api.clj but even clj-kondo complains about the namespace mismatch and then I can't load the ns in the REPL

which task are we talking about?

are you copying src dirs or compiling clj to classes?

if the former, you can selectively copy whatever you want. if the latter, you can selectively compile whatever you want

I think I figured it out but I suppose it would be both/either of b/write-pom and b/copy-dir. Should my POM also be modified in <sourceDirectory> ?

write-pom just write stuff in the META-INF, so this seems likely a completely different question than prior. the pom template is assumed to be in <root>/pom.xml but you can specify it to read from wherever you want

if you are only including a subset of your source, you may find it helpful for your sanity to split that into separate directory roots

I see. I thought b/write-pom had some bearing on the root pom.xml but TIL.

https://clojure.github.io/tools.build/clojure.tools.build.api.html#var-write-pom

reads template from :src-pom, modifies based on basis and other args, writes to :class-dir

Thanks for the clarification 🙏:skin-tone-2: I'll have to play around, really have not turned any tools-build knobs yet