Apologies, I don’t have a lot of time to dig into this further and my memory has faded since I last ran into this, but I remember at least two issues:

• when I want to use a :git/url version of a library that’s built with lein, I have to use :deps/manifest :deps and I believe that there’s basically no way for clj to know about the dependencies of the library that way (keep in mind that pom.xml is not usually checked into git for these libraries). The way I used this was to override the fi.metosin/reitit-openapi transitive sub-module of fi.metosin/reitit (which I got from clojars), so I already had all the other dependencies in the classpath.

• I had a private fork of a library that was built with lein and was relying on build steps that could have been solved :deps/prep-lib if the lib was using tools deps

The reasons I had to use git refs and private forks are fixed now in the upstream of the libraries so I don’t have my workarounds anymore.

It may sound bad, but I agree. The split between tools deps and lein just creates confusion and friction with newcomers, who start using clojure with deps, but inevitably run into a library that’s built with lein. Also, mixing lein dependencies into a tools deps project breaks things like overriding transitive dependencies.