Are there circumstances in which the REPL run configuration dialog does not offer the 'How to run it' section with the input to supply e.g. deps aliases?
It seems that some modules in my project permit it and others do not.
Are those modules imported as deps modules? That option will be disabled for lein/maven/other modules. That's the only condition I can see in the code that would cause what you're seeing.
Yes! that's it, thank you. It was showing as a module (in a complex multi-module project) but I think only because it was depended on as a local/root by another module. Once I added it as it's own module it started behaving more as I expected.
Tangentially, should the 'Add as Clojure Deps Project' option on the right-click menu in the project view be labelled 'Add as Clojure Deps Module'?
So, that's a thorny question, which I'm not really sure how to answer. All the lein/deps terminology uses "project" for what is conceptually a bunch of code managed by a project.clj/deps.edn. But that's different from what IntelliJ uses Project for, which is more like a monorepo, and an IntelliJ Module is more like a lein/deps project. I'm still unsure whether to use Clojure-focused or IntelliJ-focused terminology here, and I suspect that I use the two in inconsistent ways in various places.
Adding it as a <thing> seems like an intellij action to me, focused on making the IDE understand it, so that you can get IDE benefits. To my mind you are adding a Clojure 'Project' as an IntelliJ 'Module'. Personally I think I'd find 'module' less confusing, but I appreciate that changing it now might be the most confusing!