Preserve transitive dependency tree by using :managed-dependencies

[RickMoynihan]

lein-tools-deps currently works by asking tools.deps to resolve all dependencies before adding them and all their transitive dependencies flattened into leiningen's :dependencies vector.

This guarantees leiningen picks the same versions of transitive dependencies as tools.deps, but it does mean if you're using lein-tools-deps to produce a library, all your transitive dependencies are lifted; which makes resolving dependencies conflicts through :exclusions etc much harder for your consumers.

@favila suggested a potential solution to this, which is to load all deps into :managed-dependencies and just the immediate roots from deps.edn into :dependencies. This should both guarantee the same resolution, and preserve the hierarchy of the transitive dependency tree, and make lein-tools-deps much more suitable for publishing libraries.

[RickMoynihan]

You can see some of the effects of this issue described here