diff --git a/build-tools-internal/src/main/groovy/elasticsearch.ide.gradle b/build-tools-internal/src/main/groovy/elasticsearch.ide.gradle
index eb3a529498fa7..60ae4d58f343e 100644
--- a/build-tools-internal/src/main/groovy/elasticsearch.ide.gradle
+++ b/build-tools-internal/src/main/groovy/elasticsearch.ide.gradle
@@ -166,7 +166,7 @@ if (providers.systemProperty('idea.active').getOrNull() == 'true') {
   tasks.register('buildDependencyArtifacts') {
     group = 'ide'
     description = 'Builds artifacts needed as dependency for IDE modules'
-    dependsOn([':plugins:repository-hdfs:hadoop-client-api:shadowJar',
+    dependsOn([':plugins:repository-hdfs:hadoop-client-api:jar',
       ':x-pack:plugin:esql:compute:ann:jar',
       ':x-pack:plugin:esql:compute:gen:jar',
       ':server:generateModulesList',
diff --git a/plugins/repository-hdfs/hadoop-client-api/build.gradle b/plugins/repository-hdfs/hadoop-client-api/build.gradle
index c20d391e6bedd..c156e44d2f06f 100644
--- a/plugins/repository-hdfs/hadoop-client-api/build.gradle
+++ b/plugins/repository-hdfs/hadoop-client-api/build.gradle
@@ -21,22 +21,27 @@ dependencies {
 
 def outputDir = layout.buildDirectory.dir("patched-classes")
 
-def patchTask = tasks.register("patchClasses", JavaExec)
-patchTask.configure {
-  dependsOn configurations.thejar, sourceSets.patcher.getCompileJavaTaskName()
+def patchTask = tasks.register("patchClasses", JavaExec) {
+  inputs.files(configurations.thejar).withPathSensitivity(PathSensitivity.RELATIVE)
+  inputs.files(sourceSets.patcher.output).withPathSensitivity(PathSensitivity.RELATIVE)
   outputs.dir(outputDir)
   classpath = sourceSets.patcher.runtimeClasspath
   mainClass = 'org.elasticsearch.hdfs.patch.HdfsClassPatcher'
   doFirst {
-    args configurations.thejar.singleFile, outputDir.get().getAsFile().toString()
+    args(configurations.thejar.singleFile, outputDir.get().asFile)
   }
 }
 
 tasks.named('jar').configure {
   dependsOn(patchTask)
   dependsOn(configurations.thejar)
-  duplicatesStrategy = DuplicatesStrategy.EXCLUDE
 
-  from(outputDir) // patch directory first so any files patched are excluded as duplicates
-  from(project.zipTree(configurations.thejar.singleFile))
+  from(outputDir)
+  from({ project.zipTree(configurations.thejar.singleFile) }) {
+    eachFile {
+      if (outputDir.get().file(it.relativePath.pathString).asFile.exists()) {
+        it.exclude()
+      }
+    }
+  }
 }