diff --git a/build.gradle b/build.gradle
index 14d9be8e264..34277fbe60f 100644
--- a/build.gradle
+++ b/build.gradle
@@ -3,7 +3,10 @@ description = 'Builds the Machine Learning Java classes and UI'
 import org.gradle.plugins.ide.eclipse.model.SourceFolder
 import org.elasticsearch.gradle.precommit.LicenseHeadersTask
 import org.elasticsearch.gradle.VersionProperties
-import org.apache.tools.ant.taskdefs.condition.Os
+
+if (project.projectDir.name != 'prelert-legacy') {
+  throw new GradleException('You must checkout prelert-legacy in the following directory: <path to Elasticsearch checkout>/../elasticsearch-extra/prelert-legacy')
+}
 
 String mlAwsAccessKey = System.env.PRELERT_AWS_ACCESS_KEY_ID
 if (mlAwsAccessKey == null && project.hasProperty("PRELERT_AWS_ACCESS_KEY_ID")) {
@@ -26,40 +29,6 @@ if (envCppLocalDists != null) {
 
 allprojects {
   group = 'org.elasticsearch.ml'
-  version = VersionProperties.elasticsearch
-}
-
-configurations.all {
-    // check for updates every build
-    resolutionStrategy.cacheChangingModulesFor 0, 'seconds'
-}
-
-buildscript {
-    repositories {
-        if (System.getProperty("repos.mavenlocal") != null) {
-            // with -Drepos.mavenlocal=true we can force checking the local .m2 repo which is useful for building against
-            // elasticsearch snapshots
-            mavenLocal()
-        }
-        mavenCentral()
-        maven {
-            name 'sonatype-snapshots'
-            url "https://oss.sonatype.org/content/repositories/snapshots/"
-        }
-        jcenter()
-    }
-    dependencies {
-        classpath group: 'org.elasticsearch.gradle', name: 'build-tools', version: "${elasticsearchVersion}", changing: true
-    }
-}
-
-subprojects {
-  // we must not publish to sonatype until we have set up x-plugins to only publish the parts we want to publish!
-  project.afterEvaluate {
-    if (project.plugins.hasPlugin('com.bmuschko.nexus') && project.nexus.repositoryUrl.startsWith('file://') == false) {
-      uploadArchives.enabled = false
-    }
-  }
 }
 
 task bundlePack(type: Zip) {
@@ -70,7 +39,31 @@ task bundlePack(type: Zip) {
   from { zipTree(project('kibana').bundlePlugin.outputs.files.singleFile) }
   destinationDir file('build/distributions')
   baseName = 'ml'
-  version = project.version
+  version = VersionProperties.elasticsearch
+}
+
+subprojects {
+  plugins.withType(MavenPublishPlugin).whenPluginAdded {
+    publishing {
+      publications {
+        // add license information to generated poms
+        all {
+          pom.withXml { XmlProvider xml ->
+            Node node = xml.asNode()
+
+            Node license = node.appendNode('licenses').appendNode('license')
+            license.appendNode('name', 'Elastic Commercial Software End User License Agreement')
+            license.appendNode('url', 'https://www.elastic.co/eula/')
+            license.appendNode('distribution', 'repo')
+
+            Node developer = node.appendNode('developers').appendNode('developer')
+            developer.appendNode('name', 'Elastic')
+            developer.appendNode('url', 'http://www.elastic.co')
+          }
+        }
+      }
+    }
+  }
 }
 
 task assemble(dependsOn: bundlePack) {
@@ -83,11 +76,6 @@ task test(dependsOn: [':elasticsearch:test', ':kibana:test']) {
   description = 'Assembles and tests this project.'
 }
 
-task build(dependsOn: [assemble, test]) {
-  group = 'Build'
-  description = 'Assembles and tests this project.'
-}
-
 task clean(type: Delete) {
   group = 'Build'
   description = 'Deletes the build directory'
@@ -95,26 +83,16 @@ task clean(type: Delete) {
 }
 
 subprojects {
-    apply plugin: 'eclipse'
-    apply plugin: 'idea'
 
-    buildscript {
-        repositories {
-            if (System.getProperty("repos.mavenlocal") != null) {
-                // with -Drepos.mavenlocal=true we can force checking the local .m2 repo which is useful for building against
-                // elasticsearch snapshots
-                mavenLocal()
-            }
-            mavenCentral()
-            maven {
-                name 'sonatype-snapshots'
-                url "https://oss.sonatype.org/content/repositories/snapshots/"
-            }
-            jcenter()
-        }
-    }
+  tasks.withType(LicenseHeadersTask.class) {
+    approvedLicenses = ['Elasticsearch Confidential']
+    additionalLicense 'ESCON', 'Elasticsearch Confidential', 'ELASTICSEARCH CONFIDENTIAL'
+  }
+  ext.projectSubstitutions += [ "org.elasticsearch.plugin:ml-api:${version}": ':prelert-legacy:elasticsearch' ]
+}
 
-    repositories {
+allprojects {
+      repositories {
         if (System.getProperty("repos.mavenlocal") != null) {
             // with -Drepos.mavenlocal=true we can force checking the local .m2 repo which is useful for building against
             // elasticsearch snapshots
@@ -134,103 +112,4 @@ subprojects {
         }
         jcenter()
     }
-
-    tasks.withType(LicenseHeadersTask.class) {
-      approvedLicenses = ['Elasticsearch Confidential']
-      additionalLicense 'ESCON', 'Elasticsearch Confidential', 'ELASTICSEARCH CONFIDENTIAL'
-    }
-}
-
-allprojects {
-  // injecting groovy property variables into all projects
-  project.ext {
-    // for ide hacks...
-    isEclipse = System.getProperty("eclipse.launcher") != null || gradle.startParameter.taskNames.contains('eclipse') || gradle.startParameter.taskNames.contains('cleanEclipse')
-    isIdea = System.getProperty("idea.active") != null || gradle.startParameter.taskNames.contains('idea') || gradle.startParameter.taskNames.contains('cleanIdea')
-  }
-}
-
-allprojects {
-  apply plugin: 'idea'
-
-  if (isIdea) {
-    project.buildDir = file('build-idea')
-  }
-  idea {
-    module {
-      inheritOutputDirs = false
-      outputDir = file('build-idea/classes/main')
-      testOutputDir = file('build-idea/classes/test')
-
-      // also ignore other possible build dirs
-      excludeDirs += file('build')
-      excludeDirs += file('build-eclipse')
-
-      iml {
-        // fix so that Gradle idea plugin properly generates support for resource folders
-        // see also https://issues.gradle.org/browse/GRADLE-2975
-        withXml {
-          it.asNode().component.content.sourceFolder.findAll { it.@url == 'file://$MODULE_DIR$/src/main/resources' }.each {
-            it.attributes().remove('isTestSource')
-            it.attributes().put('type', 'java-resource')
-          }
-          it.asNode().component.content.sourceFolder.findAll { it.@url == 'file://$MODULE_DIR$/src/test/resources' }.each {
-            it.attributes().remove('isTestSource')
-            it.attributes().put('type', 'java-test-resource')
-          }
-        }
-      }
-    }
-  }
-}
-
-// Make sure gradle idea was run before running anything in intellij (including import).
-File ideaMarker = new File(projectDir, '.local-idea-is-configured')
-tasks.idea.doLast {
-  ideaMarker.setText('', 'UTF-8')
-}
-if (System.getProperty('idea.active') != null && ideaMarker.exists() == false) {
-  throw new GradleException('You must run gradle idea from the root of elasticsearch before importing into IntelliJ')
-}
-
-// eclipse configuration
-allprojects {
-  apply plugin: 'eclipse'
-  // Name all the non-root projects after their path so that paths get grouped together when imported into eclipse.
-  if (path != ':') {
-    eclipse.project.name = path
-    if (Os.isFamily(Os.FAMILY_WINDOWS)) {
-      eclipse.project.name = eclipse.project.name.replace(':', '_')
-    }
-  }
-
-  plugins.withType(JavaBasePlugin) {
-    File eclipseBuild = project.file('build-eclipse')
-    eclipse.classpath.defaultOutputDir = eclipseBuild
-    if (isEclipse) {
-      // set this so generated dirs will be relative to eclipse build
-      project.buildDir = eclipseBuild
-    }
-    eclipse.classpath.file.whenMerged { classpath ->
-      // give each source folder a unique corresponding output folder
-      int i = 0;
-      classpath.entries.findAll { it instanceof SourceFolder }.each { folder ->
-        i++;
-        // this is *NOT* a path or a file.
-        folder.output = "build-eclipse/" + i
-      }
-    }
-  }
-  task copyEclipseSettings(type: Copy) {
-    // TODO: "package this up" for external builds
-    from new File(project.rootDir, 'buildSrc/src/main/resources/eclipse.settings')
-    into '.settings'
-  }
-  // otherwise .settings is not nuked entirely
-  task wipeEclipseSettings(type: Delete) {
-    delete '.settings'
-  }
-  tasks.cleanEclipse.dependsOn(wipeEclipseSettings)
-  // otherwise the eclipse merging is *super confusing*
-  tasks.eclipse.dependsOn(cleanEclipse, copyEclipseSettings)
 }
diff --git a/buildSrc/settings.gradle b/buildSrc/settings.gradle
new file mode 100644
index 00000000000..62e17df68b1
--- /dev/null
+++ b/buildSrc/settings.gradle
@@ -0,0 +1,10 @@
+File extrasDir = new File(settingsDir, '../..').getCanonicalFile()
+if (extrasDir.name.endsWith('-extra') == false) {
+  throw new GradleException("prelert-legacy must be checked out under an elasticsearch-extra directory, found ${extrasDir.name}")
+}
+File elasticsearchDir = new File(extrasDir.parentFile, extrasDir.name[0..-7])
+if (elasticsearchDir.exists() == false) {
+  throw new GradleException("${elasticsearchDir.name} is missing as a sibling to ${extrasDir.name}")
+}
+
+project(':').projectDir = new File(elasticsearchDir, 'buildSrc')
diff --git a/dev-tools/ci b/dev-tools/ci
new file mode 100755
index 00000000000..633271d518e
--- /dev/null
+++ b/dev-tools/ci
@@ -0,0 +1,151 @@
+#!/bin/bash
+# This script is used as a single command to run the ml tests.
+#
+# It will attempt to check out 'elasticsearch' into a sibling directory
+# unless the environment variable `USE_EXISTING_ES` has a value. The
+# branch of elasticsearch which will be checked out depends on
+# environment variables. If running locally, set GIT_BRANCH. When
+# running in Jenkins, that env var is set. When running a PR
+# jenkins job, the variables PR_SOURCE_BRANCH and PR_TARGET_BRANCH
+# will be set and the source branch will be looked for in elasticsearch
+# before falling back to the target branch name.
+#
+# It will also attempt to install the appropriate version of node.js
+# for the Kibana plugin tests using nvm, unless
+# `xpack.kibana.build=false` is defined in
+# ~/.gradle/gradle.properties. Set a custom nvm directory using the
+# `NVM_DIR` environment variable.
+#
+
+# Turn on semi-strict mode
+set -e
+set -o pipefail
+
+# Allow the user choose different test through a single cli arg
+# default to `check` if no argument has been supplied
+key=${1-check}
+case $key in
+    packagingTest)
+        GRADLE_CLI_ARGS=(
+            "--info"
+            "-Pvagrant.boxes=all"
+            ":prelert-legacy:qa:vagrant:packagingTest"
+        )
+        ;;
+    check)
+        GRADLE_CLI_ARGS=(
+            "--info"
+            "check"
+            "-Dtests.network=true"
+            "-Dtests.badapples=true"
+        )
+        ;;
+    jdk9)
+        GRADLE_CLI_ARGS=(
+            "-Pxpack.kibana.build=false"
+            "--info"
+            "check"
+            "-Dtests.network=true"
+            "-Dtests.badapples=true"
+            -Dtests.jvm.argline="--add-opens=java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.net=ALL-UNNAMED --add-opens=java.base/java.nio=ALL-UNNAMED --add-opens=java.base/java.nio.file=ALL-UNNAMED --add-opens=java.base/java.security.cert=ALL-UNNAMED --add-opens=java.base/java.util=ALL-UNNAMED --add-opens=java.base/javax.net.ssl=ALL-UNNAMED"
+        )
+        ;;
+    *)
+        echo "Unsupported cli argument $1. Allowed arguments are packagingTest or check. No argument defaults to check."
+        exit 1;;
+esac
+
+SCRIPT="$0"
+
+# SCRIPT may be an arbitrarily deep series of symlinks. Loop until we have the concrete path.
+while [ -h "$SCRIPT" ] ; do
+  ls=$(ls -ld "$SCRIPT")
+  # Drop everything prior to ->
+  link=$(expr "$ls" : '.*-> \(.*\)$')
+  if expr "$link" : '/.*' > /dev/null; then
+    SCRIPT="$link"
+  else
+    SCRIPT=$(dirname "$SCRIPT")/"$link"
+  fi
+done
+
+# determine base directory
+BASE_DIR=$(dirname "$SCRIPT")/..
+
+# make BASE_DIR absolute
+BASE_DIR=$(cd "$BASE_DIR"; pwd)
+
+PARENT_DIR=$(cd "$BASE_DIR"/../..; pwd)
+
+# go to the parent directory
+cd $PARENT_DIR
+
+if [ -z ${USE_EXISTING_ES:+x} ]; then
+    if [ -d "./elasticsearch" ]; then
+        echo "I expected a clean workspace but an 'elasticsearch' sibling directory already exists in [$PARENT_DIR]!"
+        echo
+        echo "Either define 'USE_EXISTING_ES' or remove the existing 'elasticsearch' sibling."
+        exit 1
+    fi
+    BRANCH=${PR_SOURCE_BRANCH:-${GIT_BRANCH#*/}} # GIT_BRANCH starts with the repo, i.e., origin/master
+    BRANCH=${BRANCH:-master} # fall back to CI branch if not testing a PR
+    echo "Checking if branch '$BRANCH' has elasticsearch sibling..."
+    ES_REPO_URL="https://github.com/elastic/elasticsearch.git"
+    if [ -z ${USE_SSH:+x} ]; then
+      ES_REPO_URL="git@github.com:elastic/elasticsearch.git"
+    fi
+    if [[ -z "$(git ls-remote --heads $ES_REPO_URL $BRANCH)" ]]; then
+      echo "No sibling branch, using PR target branch"
+      BRANCH=$PR_TARGET_BRANCH
+    fi
+    echo "Checking out Elasticsearch '$BRANCH' branch..."
+    git clone -b $BRANCH $ES_REPO_URL --depth=1
+else
+    if [ -d "./elasticsearch" ]; then
+        echo "Using existing 'elasticsearch' checkout"
+    else
+        echo "You have defined 'USE_EXISTING_ES' but no existing Elasticsearch directory exists!"
+        exit 2
+    fi
+fi
+
+ES_COMMIT="$(cd "$PARENT_DIR/elasticsearch"; git show --oneline -s | cut -d\  -f1)"
+ML_COMMIT="$(cd "$BASE_DIR"; git show --oneline -s | cut -d\  -f1)"
+
+# back to base directory
+cd "$BASE_DIR"
+
+if ! grep -q -e '^xpack\.kibana\.build=false$' ~/.gradle/gradle.properties
+then
+  # install the correct node.js version
+  if [ -z ${NVM_DIR:+x} ]; then
+    export NVM_DIR="/var/lib/jenkins/.nvm";
+  fi
+
+  NVM_SCRIPT="$NVM_DIR/nvm.sh"
+  if [ -s "$NVM_SCRIPT" ]; then
+    . "$NVM_SCRIPT"  # load nvm
+  else
+    echo "Unable to find the nvm script at \"$NVM_SCRIPT\""
+    exit 1
+  fi
+
+  echo "Installing node.js version $(cat ./kibana/.node-version)..."
+  nvm install "$(cat ./kibana/.node-version)"
+fi
+
+echo "Running ML tests..."
+echo "Running in $PWD"
+echo "Elasticsearch commit:    $ES_COMMIT"
+echo "Machine Learning commit: $ML_COMMIT"
+
+# output the commands
+set -xuf
+
+# clean
+gradle --stacktrace clean
+
+# Actually run the tests
+gradle "${GRADLE_CLI_ARGS[@]}"
+
+# ~*~ shell-script-mode ~*~
diff --git a/elasticsearch/build.gradle b/elasticsearch/build.gradle
index 3dc87c87c83..8e19e46e2e6 100644
--- a/elasticsearch/build.gradle
+++ b/elasticsearch/build.gradle
@@ -8,10 +8,6 @@ esplugin {
     classname 'org.elasticsearch.xpack.ml.MlPlugin'
 }
 
-version = project.version
-
-thirdPartyAudit.enabled = false
-
 configurations {
     nativeBundle
 }
diff --git a/qa/basic-multi-node/build.gradle b/qa/basic-multi-node/build.gradle
index 50e66b42da9..b3307b2d841 100644
--- a/qa/basic-multi-node/build.gradle
+++ b/qa/basic-multi-node/build.gradle
@@ -2,13 +2,13 @@ apply plugin: 'elasticsearch.standalone-rest-test'
 apply plugin: 'elasticsearch.rest-test'
 
 dependencies {
-    testCompile project(path: ':elasticsearch', configuration: 'runtime')
+    testCompile project(path: ':prelert-legacy:elasticsearch', configuration: 'runtime')
 }
 
 integTest {
     cluster {
         numNodes = 3
         distribution = 'zip'
-        plugin ':elasticsearch'
+        plugin ':prelert-legacy:elasticsearch'
     }
 }
diff --git a/qa/build.gradle b/qa/build.gradle
new file mode 100644
index 00000000000..e69de29bb2d
diff --git a/settings.gradle b/settings.gradle
index 8c22454279e..12c192f2125 100644
--- a/settings.gradle
+++ b/settings.gradle
@@ -1,5 +1,7 @@
-rootProject.name = 'ml'
-include ':elasticsearch'
-include ':docs'
-include ':kibana'
-include ':qa:basic-multi-node'
+File extrasDir = new File(settingsDir, '..').getCanonicalFile()
+if (extrasDir.name.endsWith('-extra') == false) {
+  throw new GradleException("prelert-legacy must be checked out under an elasticsearch-extra directory, found ${extrasDir.name}")
+}
+File elasticsearchDir = new File(extrasDir.parentFile, extrasDir.name[0..-7])
+project(':').projectDir = elasticsearchDir
+apply from: "${elasticsearchDir}/settings.gradle"