Mostly Java-based lein project with JUnit and Log4J2 (main.clj is still entry point)

project.clj

(defproject com.example/foo "0.1.0"
  :description "Does fooness"
  :url "http://example.com/"
  :license {:name "Copyright ©2014 Josh Graham"}
  :aliases {"dist" ["do" ["clean"] ["test"] ["uberjar"]]                                                                ;$ lein dist # create distribution JAR
            "debug" ["with-profile" "dev,debug" "run"]}                                                                 ;$ lein debug # run for a 'remote' debugger
  :aot :all
  :auto-clean false                                                                                                     ;"dist" alias does the full cycle
  :clean-targets ^{:protect false} [:target-path :junit-results-dir]
  :dependencies [
                 [org.clojure/clojure "1.8.0"]
                 [joda-time/joda-time "2.5"]
                 ;; Logging
                 [org.clojure/tools.logging "0.3.1"]
                 [org.slf4j/slf4j-api "1.7.21"]
                 [org.slf4j/jcl-over-slf4j "1.7.21"]
                 [org.slf4j/jul-to-slf4j "1.7.21"]
                 [org.apache.logging.log4j/log4j-core "2.8.2"]
                 [org.apache.logging.log4j/log4j-slf4j-impl "2.8.2"]
                 [com.fasterxml.jackson.core/jackson-core "2.8.8"]
                 [com.fasterxml.jackson.core/jackson-databind "2.8.8"]
                 [com.fasterxml.jackson.dataformat/jackson-dataformat-yaml "2.8.8"]
                 [com.lmax/disruptor "3.3.0"]
                ]
  :deploy-branches ["master"]
  :eval-in :nrepl
  :injections [(require 'clojure.pprint)]
  :java-source-paths ["src" "test"]
  :javac-options ["-target" "1.8" "-source" "1.8" "-Xlint:-options" "-Xlint:unchecked" "-XDignore.symbol.file"]         ;warn, except about proprietary API use
  :junit ["test"]
  :junit-formatter "xml"
  :junit-results-dir "test-results"
  :jvm-opts ["-DLog4jContextSelector=org.apache.logging.log4j.core.async.AsyncLoggerContextSelector"]
  :main foo.main
  :omit-source true
  :plugins [
            [lein-environ "1.0.0"]
            [lein-junit "1.1.8"]
            [lein-pprint "1.1.2"]
            ]
  :pom-location "target"
  :profiles {:dev {:dependencies [
                                  [junit/junit "4.11"]                                                                  ;JUnit testing
                                  [org.clojure/tools.nrepl "0.2.5"]
                                  [org.hamcrest/hamcrest-all "1.3"]
                                  [org.mockito/mockito-core "1.10.19"]
                                  ]}
             :debug {:jvm-opts ["-agentlib:jdwp=transport=dt_socket,server=y,suspend=y,address=5005"]}
             :uberjar {:aot :all}}
  :release-tasks [
                  ["vcs" "assert-committed"]
                  ["change" "version" "leiningen.release/bump-version" "release"]
                  ["vcs" "commit"]
                  ["vcs" "tag"]
                  ]
  :repositories {"m2" "file://$HOME/.m2/repository"}
  :resource-paths ["resources"]
  :target-path "target"
  :uberjar-exclusions [#".*/?junit" #"^clojure/test" #"^foo/.*Test"]                                                             ;Remove our testing artifacts
  :uberjar-name "foo.jar"
  )

Directory structure looks like this:

/
  resources/
  src/
    foo/
  target/
  test/
    foo/
  test-results/
  project.clj

The src/ is a source root and test/ is a test source root. The foo/ in both are package directories (no need for long, unwieldy, FQDN-based package names in micro-services). Java and Clojure source files live in the same directories.