diff --git a/benchmarks/build.gradle b/benchmarks/build.gradle
index e7ee5a059ab37..80d1982300dd1 100644
--- a/benchmarks/build.gradle
+++ b/benchmarks/build.gradle
@@ -17,17 +17,6 @@
  * under the License.
  */
 
-buildscript {
-    repositories {
-        maven {
-            url 'https://plugins.gradle.org/m2/'
-        }
-    }
-    dependencies {
-        classpath 'com.github.jengelman.gradle.plugins:shadow:2.0.4'
-    }
-}
-
 apply plugin: 'elasticsearch.build'
 
 // order of this section matters, see: https://github.com/johnrengelman/shadow/issues/336
@@ -81,10 +70,6 @@ thirdPartyAudit.excludes = [
         'org.openjdk.jmh.util.Utils'
 ]
 
-shadowJar {
-    classifier = 'benchmarks'
-}
-
 runShadow {
     executable = new File(project.runtimeJavaHome, 'bin/java')
 }
diff --git a/build.gradle b/build.gradle
index 187e247705277..ccbb6898dc413 100644
--- a/build.gradle
+++ b/build.gradle
@@ -17,7 +17,7 @@
  * under the License.
  */
 
-
+import com.github.jengelman.gradle.plugins.shadow.ShadowPlugin
 import org.apache.tools.ant.taskdefs.condition.Os
 import org.apache.tools.ant.filters.ReplaceTokens
 import org.elasticsearch.gradle.BuildPlugin
@@ -303,18 +303,55 @@ subprojects {
     if (project.plugins.hasPlugin(BuildPlugin)) {
       String artifactsHost = VersionProperties.elasticsearch.isSnapshot() ? "https://snapshots.elastic.co" : "https://artifacts.elastic.co"
       Closure sortClosure = { a, b -> b.group <=> a.group }
-      Closure depJavadocClosure = { dep ->
-        if (dep.group != null && dep.group.startsWith('org.elasticsearch')) {
-          Project upstreamProject = dependencyToProject(dep)
-          if (upstreamProject != null) {
-            project.javadoc.dependsOn "${upstreamProject.path}:javadoc"
-            String artifactPath = dep.group.replaceAll('\\.', '/') + '/' + dep.name.replaceAll('\\.', '/') + '/' + dep.version
-            project.javadoc.options.linksOffline artifactsHost + "/javadoc/" + artifactPath, "${upstreamProject.buildDir}/docs/javadoc/"
+      Closure depJavadocClosure = { shadowed, dep ->
+        if (dep.group == null || false == dep.group.startsWith('org.elasticsearch')) {
+          return
+        }
+        Project upstreamProject = dependencyToProject(dep)
+        if (upstreamProject == null) {
+          return
+        }
+        if (shadowed) {
+          /*
+           * Include the source of shadowed upstream projects so we don't
+           * have to publish their javadoc.
+           */
+          project.evaluationDependsOn(upstreamProject.path)
+          project.javadoc.source += upstreamProject.javadoc.source
+          /*
+           * Do not add those projects to the javadoc classpath because
+           * we are going to resolve them with their source instead.
+           */
+          project.javadoc.classpath = project.javadoc.classpath.filter { f ->
+            false == upstreamProject.configurations.archives.artifacts.files.files.contains(f)
           }
+          /*
+           * Instead we need the upstream project's javadoc classpath so
+           * we don't barf on the classes that it references.
+           */
+          project.javadoc.classpath += upstreamProject.javadoc.classpath
+        } else {
+          // Link to non-shadowed dependant projects
+          project.javadoc.dependsOn "${upstreamProject.path}:javadoc"
+          String artifactPath = dep.group.replaceAll('\\.', '/') + '/' + dep.name.replaceAll('\\.', '/') + '/' + dep.version
+          project.javadoc.options.linksOffline artifactsHost + "/javadoc/" + artifactPath, "${upstreamProject.buildDir}/docs/javadoc/"
         }
       }
-      project.configurations.compile.dependencies.findAll().toSorted(sortClosure).each(depJavadocClosure)
-      project.configurations.compileOnly.dependencies.findAll().toSorted(sortClosure).each(depJavadocClosure)
+      boolean hasShadow = project.plugins.hasPlugin(ShadowPlugin)
+      project.configurations.compile.dependencies
+          .findAll()
+          .toSorted(sortClosure)
+          .each({ c -> depJavadocClosure(hasShadow, c) })
+      project.configurations.compileOnly.dependencies
+          .findAll()
+          .toSorted(sortClosure)
+          .each({ c -> depJavadocClosure(hasShadow, c) })
+      if (hasShadow) {
+        project.configurations.shadow.dependencies
+            .findAll()
+            .toSorted(sortClosure)
+            .each({ c -> depJavadocClosure(false, c) })
+      }
     }
   }
 }
diff --git a/buildSrc/build.gradle b/buildSrc/build.gradle
index 3d100daf7d65f..eb95ff148f63c 100644
--- a/buildSrc/build.gradle
+++ b/buildSrc/build.gradle
@@ -104,6 +104,7 @@ dependencies {
   compile 'de.thetaphi:forbiddenapis:2.5'
   compile 'org.apache.rat:apache-rat:0.11'
   compile "org.elasticsearch:jna:4.5.1"
+  compile 'com.github.jengelman.gradle.plugins:shadow:2.0.4'
   testCompile "junit:junit:${props.getProperty('junit')}"
 }
 
diff --git a/buildSrc/src/main/groovy/org/elasticsearch/gradle/BuildPlugin.groovy b/buildSrc/src/main/groovy/org/elasticsearch/gradle/BuildPlugin.groovy
index 89e10c50ff782..b5b5ec95becc9 100644
--- a/buildSrc/src/main/groovy/org/elasticsearch/gradle/BuildPlugin.groovy
+++ b/buildSrc/src/main/groovy/org/elasticsearch/gradle/BuildPlugin.groovy
@@ -19,6 +19,7 @@
 package org.elasticsearch.gradle
 
 import com.carrotsearch.gradle.junit4.RandomizedTestingTask
+import com.github.jengelman.gradle.plugins.shadow.ShadowPlugin
 import org.apache.tools.ant.taskdefs.condition.Os
 import org.eclipse.jgit.lib.Constants
 import org.eclipse.jgit.lib.RepositoryBuilder
@@ -36,12 +37,14 @@ import org.gradle.api.artifacts.ModuleDependency
 import org.gradle.api.artifacts.ModuleVersionIdentifier
 import org.gradle.api.artifacts.ProjectDependency
 import org.gradle.api.artifacts.ResolvedArtifact
+import org.gradle.api.artifacts.SelfResolvingDependency
 import org.gradle.api.artifacts.dsl.RepositoryHandler
 import org.gradle.api.execution.TaskExecutionGraph
 import org.gradle.api.plugins.JavaPlugin
 import org.gradle.api.publish.maven.MavenPublication
 import org.gradle.api.publish.maven.plugins.MavenPublishPlugin
 import org.gradle.api.publish.maven.tasks.GenerateMavenPom
+import org.gradle.api.tasks.SourceSet
 import org.gradle.api.tasks.bundling.Jar
 import org.gradle.api.tasks.compile.GroovyCompile
 import org.gradle.api.tasks.compile.JavaCompile
@@ -498,7 +501,41 @@ class BuildPlugin implements Plugin<Project> {
                     }
                 }
             }
+            project.plugins.withType(ShadowPlugin).whenPluginAdded {
+                project.publishing {
+                    publications {
+                        nebula(MavenPublication) {
+                            artifact project.tasks.shadowJar
+                            artifactId = project.archivesBaseName
+                            /*
+                            * Configure the pom to include the "shadow" as compile dependencies
+                            * because that is how we're using them but remove all other dependencies
+                            * because they've been shaded into the jar.
+                            */
+                            pom.withXml { XmlProvider xml ->
+                                Node root = xml.asNode()
+                                root.remove(root.dependencies)
+                                Node dependenciesNode = root.appendNode('dependencies')
+                                project.configurations.shadow.allDependencies.each {
+                                    if (false == it instanceof SelfResolvingDependency) {
+                                        Node dependencyNode = dependenciesNode.appendNode('dependency')
+                                        dependencyNode.appendNode('groupId', it.group)
+                                        dependencyNode.appendNode('artifactId', it.name)
+                                        dependencyNode.appendNode('version', it.version)
+                                        dependencyNode.appendNode('scope', 'compile')
+                                    }
+                                }
+                                // Be tidy and remove the element if it is empty
+                                if (dependenciesNode.children.empty) {
+                                    root.remove(dependenciesNode)
+                                }
+                            }
+                        }
+                    }
+                }
+            }
         }
+
     }
 
     /** Adds compiler settings to the project */
@@ -660,6 +697,28 @@ class BuildPlugin implements Plugin<Project> {
                 }
             }
         }
+        project.plugins.withType(ShadowPlugin).whenPluginAdded {
+            /*
+             * When we use the shadow plugin we entirely replace the
+             * normal jar with the shadow jar so we no longer want to run
+             * the jar task.
+             */
+            project.tasks.jar.enabled = false
+            project.tasks.shadowJar {
+                /*
+                 * Replace the default "shadow" classifier with null
+                 * which will leave the classifier off of the file name.
+                 */
+                classifier = null
+                /*
+                 * Not all cases need service files merged but it is
+                 * better to be safe
+                 */
+                mergeServiceFiles()
+            }
+            // Make sure we assemble the shadow jar
+            project.tasks.assemble.dependsOn project.tasks.shadowJar
+        }
     }
 
     /** Returns a closure of common configuration shared by unit and integration tests. */
@@ -744,6 +803,18 @@ class BuildPlugin implements Plugin<Project> {
             }
 
             exclude '**/*$*.class'
+
+            project.plugins.withType(ShadowPlugin).whenPluginAdded {
+                /*
+                 * If we make a shaded jar we test against it.
+                 */
+                classpath -= project.tasks.compileJava.outputs.files
+                classpath -= project.configurations.compile
+                classpath -= project.configurations.runtime
+                classpath += project.configurations.shadow
+                classpath += project.tasks.shadowJar.outputs.files
+                dependsOn project.tasks.shadowJar
+            }
         }
     }
 
@@ -766,7 +837,26 @@ class BuildPlugin implements Plugin<Project> {
             additionalTest.dependsOn(project.tasks.testClasses)
             test.dependsOn(additionalTest)
         });
-        return test
+
+        project.plugins.withType(ShadowPlugin).whenPluginAdded {
+            /*
+             * We need somewhere to configure dependencies that we don't wish
+             * to shade into the jar. The shadow plugin creates a "shadow"
+             * configuration which  is *almost* exactly that. It is never
+             * bundled into the shaded jar but is used for main source
+             * compilation. Unfortunately, by default it is not used for
+             * *test* source compilation and isn't used in tests at all. This
+             * change makes it available for test compilation.
+             *
+             * Note that this isn't going to work properly with qa projects
+             * but they have no business applying the shadow plugin in the
+             * firstplace.
+             */
+            SourceSet testSourceSet = project.sourceSets.findByName('test')
+            if (testSourceSet != null) {
+                testSourceSet.compileClasspath += project.configurations.shadow
+            }
+        }
     }
 
     private static configurePrecommit(Project project) {
diff --git a/buildSrc/src/main/groovy/org/elasticsearch/gradle/plugin/PluginBuildPlugin.groovy b/buildSrc/src/main/groovy/org/elasticsearch/gradle/plugin/PluginBuildPlugin.groovy
index eb4da8d1f314c..d76084bf22e07 100644
--- a/buildSrc/src/main/groovy/org/elasticsearch/gradle/plugin/PluginBuildPlugin.groovy
+++ b/buildSrc/src/main/groovy/org/elasticsearch/gradle/plugin/PluginBuildPlugin.groovy
@@ -18,11 +18,13 @@
  */
 package org.elasticsearch.gradle.plugin
 
+import com.github.jengelman.gradle.plugins.shadow.ShadowPlugin
 import nebula.plugin.info.scm.ScmInfoPlugin
 import org.elasticsearch.gradle.BuildPlugin
 import org.elasticsearch.gradle.NoticeTask
 import org.elasticsearch.gradle.test.RestIntegTestTask
 import org.elasticsearch.gradle.test.RunTask
+import org.gradle.api.InvalidUserDataException
 import org.gradle.api.JavaVersion
 import org.gradle.api.Project
 import org.gradle.api.Task
@@ -46,6 +48,18 @@ public class PluginBuildPlugin extends BuildPlugin {
     @Override
     public void apply(Project project) {
         super.apply(project)
+        project.plugins.withType(ShadowPlugin).whenPluginAdded {
+            /*
+             * We've not tested these plugins together and we're fairly sure
+             * they aren't going to work properly as is *and* we're not really
+             * sure *why* you'd want to shade stuff in plugins. So we throw an
+             * exception here to make you come and read this comment. If you
+             * have a need for shadow while building plugins then know that you
+             * are probably going to have to fight with gradle for a while....
+             */
+            throw new InvalidUserDataException('elasticsearch.esplugin is not '
+                    + 'compatible with com.github.johnrengelman.shadow');
+        }
         configureDependencies(project)
         // this afterEvaluate must happen before the afterEvaluate added by integTest creation,
         // so that the file name resolution for installing the plugin will be setup
diff --git a/client/benchmark/build.gradle b/client/benchmark/build.gradle
index 77867f5e273f2..0c3238d985346 100644
--- a/client/benchmark/build.gradle
+++ b/client/benchmark/build.gradle
@@ -17,18 +17,6 @@
  * under the License.
  */
 
-buildscript {
-  repositories {
-    maven {
-      url 'https://plugins.gradle.org/m2/'
-    }
-  }
-  dependencies {
-    classpath 'com.github.jengelman.gradle.plugins:shadow:2.0.4'
-  }
-}
-
-
 apply plugin: 'elasticsearch.build'
 // build an uberjar with all benchmarks
 apply plugin: 'com.github.johnrengelman.shadow'
diff --git a/client/rest-high-level/build.gradle b/client/rest-high-level/build.gradle
index 2fed806e98c57..a1260894bf7aa 100644
--- a/client/rest-high-level/build.gradle
+++ b/client/rest-high-level/build.gradle
@@ -21,17 +21,6 @@ import org.elasticsearch.gradle.precommit.PrecommitTasks
 import org.elasticsearch.gradle.test.RestIntegTestTask
 import org.gradle.api.internal.provider.Providers
 
-buildscript {
-  repositories {
-    maven {
-      url 'https://plugins.gradle.org/m2/'
-    }
-  }
-  dependencies {
-    classpath 'com.github.jengelman.gradle.plugins:shadow:2.0.4'
-  }
-}
-
 apply plugin: 'elasticsearch.build'
 apply plugin: 'elasticsearch.rest-test'
 apply plugin: 'nebula.maven-base-publish'
@@ -45,49 +34,6 @@ archivesBaseName = 'elasticsearch-rest-high-level-client'
 Task copyRestSpec = RestIntegTestTask.createCopyRestSpecTask(project, Providers.FALSE)
 test.dependsOn(copyRestSpec)
 
-publishing {
-  publications {
-    nebula(MavenPublication) {
-      artifact shadowJar
-      artifactId = archivesBaseName
-      /*
-       * Configure the pom to include the "shadow" as compile dependencies
-       * because that is how we're using them but remove all other dependencies
-       * because they've been shaded into the jar.
-       */
-      pom.withXml { XmlProvider xml ->
-        Node root = xml.asNode()
-        root.remove(root.dependencies)
-        Node dependenciesNode = root.appendNode('dependencies')
-        project.configurations.shadow.allDependencies.each {
-          if (false == it instanceof SelfResolvingDependency) {
-            Node dependencyNode = dependenciesNode.appendNode('dependency')
-            dependencyNode.appendNode('groupId', it.group)
-            dependencyNode.appendNode('artifactId', it.name)
-            dependencyNode.appendNode('version', it.version)
-            dependencyNode.appendNode('scope', 'compile')
-          }
-        }
-      }
-    }
-  }
-}
-
-/*
- * We need somewhere to configure dependencies that we don't wish to shade
- * into the high level REST client. The shadow plugin creates a "shadow"
- * configuration which is *almost* exactly that. It is never bundled into
- * the shaded jar but is used for main source compilation. Unfortunately,
- * by default it is not used for *test* source compilation and isn't used
- * in tests at all. This change makes it available for test compilation.
- * A change below makes it available for testing.
- */
-sourceSets {
-  test {
-    compileClasspath += configurations.shadow
-  }
-}
-
 dependencies {
   /*
    * Everything in the "shadow" configuration is *not* copied into the
@@ -124,48 +70,3 @@ forbiddenApisMain {
   signaturesURLs += [PrecommitTasks.getResource('/forbidden/http-signatures.txt')]
   signaturesURLs += [file('src/main/resources/forbidden/rest-high-level-signatures.txt').toURI().toURL()]
 }
-
-shadowJar {
-  classifier = null
-  mergeServiceFiles()
-}
-
-// We don't need normal jar, we use shadow jar instead
-jar.enabled = false
-assemble.dependsOn shadowJar
-
-javadoc {
-  /*
-   * Bundle all of the javadoc from all of the shaded projects into this one
-   * so we don't *have* to publish javadoc for all of the "client" jars.
-   */
-  configurations.compile.dependencies.all { Dependency dep ->
-    Project p = dependencyToProject(dep)
-    if (p != null) {
-      evaluationDependsOn(p.path)
-      source += p.sourceSets.main.allJava
-    }
-  }
-}
-
-/*
- * Use the jar for testing so we have tests of the bundled jar.
- * Use the "shadow" configuration for testing because we need things
- * in it.
- */
-test {
-  classpath -= compileJava.outputs.files
-  classpath -= configurations.compile
-  classpath -= configurations.runtime
-  classpath += configurations.shadow
-  classpath += shadowJar.outputs.files
-  dependsOn shadowJar
-}
-integTestRunner {
-  classpath -= compileJava.outputs.files
-  classpath -= configurations.compile
-  classpath -= configurations.runtime
-  classpath += configurations.shadow
-  classpath += shadowJar.outputs.files
-  dependsOn shadowJar
-}
diff --git a/x-pack/plugin/sql/jdbc/build.gradle b/x-pack/plugin/sql/jdbc/build.gradle
index 9d27c2030d676..a0d9b24c50729 100644
--- a/x-pack/plugin/sql/jdbc/build.gradle
+++ b/x-pack/plugin/sql/jdbc/build.gradle
@@ -1,15 +1,3 @@
-
-buildscript {
-    repositories {
-        maven {
-            url 'https://plugins.gradle.org/m2/'
-        }
-    }
-    dependencies {
-        classpath 'com.github.jengelman.gradle.plugins:shadow:2.0.4'
-    }
-}
-
 apply plugin: 'elasticsearch.build'
 apply plugin: 'nebula.maven-base-publish'
 apply plugin: 'nebula.maven-scm'
@@ -49,7 +37,6 @@ dependencyLicenses {
 }
 
 shadowJar {
-    classifier = null
     relocate 'com.fasterxml', 'org.elasticsearch.fasterxml'
 }
 
@@ -70,26 +57,3 @@ artifacts  {
     nodeps nodepsJar
     archives shadowJar
 }
-
-publishing {
-    publications {
-        nebula(MavenPublication) {
-            artifact shadowJar
-            pom.withXml {
-                // Nebula is mistakenly including all dependencies that are already shadowed into the shadow jar
-                asNode().remove(asNode().dependencies)
-            }
-        }
-    }
-}
-
-assemble.dependsOn shadowJar
-
-// Use the jar for testing so the tests are more "real"
-test {
-    classpath -= compileJava.outputs.files
-    classpath -= configurations.compile
-    classpath -= configurations.runtime
-    classpath += shadowJar.outputs.files
-    dependsOn shadowJar
-}