Occasional you do have to deal with Java's baggage in Clojure. The best example I can think of right now is the build process. The consensus is to use Maven or the Clojure tool Leiningen.
The good news is that you also get Java's "Deployment for Dummies" solutions (just copy the JAR/WAR and you're good to go), though.
Leiningen is actually pretty cool. It uses Maven under the hood (but you don't have to know that).
The nice thing is that if you suddenly decide you need to use a Java library (say, one of the Apache Commons libs), you just add one line to your project.clj file, do "lein deps" and boom, you can use the library in your project.
Having written quite a bit of software in Common Lisp, this is a welcome change.
The good news is that you also get Java's "Deployment for Dummies" solutions (just copy the JAR/WAR and you're good to go), though.