Add the java source path.

project.clj

@@ -8,6 +8,7 @@
                  [org.apache.tika/tika-core "1.28.5"]
                  [org.apache.tika/tika-langdetect "1.28.5"]]
   :main ^:skip-aot cipher-analytical-machine.core
+  :java-source-paths ["src/main/java"]
   :target-path "target/%s"
   :profiles {:uberjar {:aot :all
                        :jvm-opts ["-Dclojure.compiler.direct-linking=true"]}})