diff --git a/TODO.md b/TODO.md
index 25d795b2..2bd27c88 100644
--- a/TODO.md
+++ b/TODO.md
@@ -1,5 +1,18 @@
 To do:
 
+Android:
+
+- [ ] Dex dependencies into kobaltBuild/intermediates/pre-dexed and preserve those across builds
+- [ ] Move the calculated applicationId back into the merged AndroidManifest.xml 
+- [ ] Dex from android builder
+- [ ] Keep exploded aars between runs
+- [ ] aars keep being refetched
+- [ ] See if there is an android manifest file in builder
+
+General
+
+- [ ] Apt should run from serviceloader
+- [ ] Auto add variant
 - [ ] The test runner only selects classes with a parameterless constructor, which works for JUnit but not for TestNG
  factories
 - [ ] Add a "Auto complete Build.kt" menu in the plug-in
@@ -31,6 +44,7 @@ To do:
 
 Done:
 
+- [x] Compile with javax.tool
 - [x] Android: multiple -source/-target flags
 - [x] Dokka: allow multiple format outputs e.g `outputFormat("html", "javadoc")`
 - [x] Finish abstracting everything in `JvmCompilerPlugin`
diff --git a/kobalt/wrapper/kobalt-wrapper.properties b/kobalt/wrapper/kobalt-wrapper.properties
index 89d1cc76..55d79852 100644
--- a/kobalt/wrapper/kobalt-wrapper.properties
+++ b/kobalt/wrapper/kobalt-wrapper.properties
@@ -1 +1 @@
-kobalt.version=0.318
\ No newline at end of file
+kobalt.version=0.320
\ No newline at end of file
diff --git a/src/main/kotlin/com/beust/kobalt/Variant.kt b/src/main/kotlin/com/beust/kobalt/Variant.kt
index fe5a5442..6c0ffff7 100644
--- a/src/main/kotlin/com/beust/kobalt/Variant.kt
+++ b/src/main/kotlin/com/beust/kobalt/Variant.kt
@@ -3,6 +3,7 @@ package com.beust.kobalt
 import com.beust.kobalt.api.*
 import com.beust.kobalt.misc.KFiles
 import com.beust.kobalt.misc.log
+import com.beust.kobalt.plugin.android.AndroidConfig
 import com.beust.kobalt.plugin.android.AndroidPlugin
 import java.io.File
 
@@ -122,23 +123,35 @@ class Variant(val initialProductFlavor: ProductFlavorConfig? = null,
         return result
     }
 
+    fun applicationId(androidConfig: AndroidConfig?): String? {
+        val mainId = productFlavor.applicationId ?: androidConfig?.applicationId
+        val result =
+            if (mainId != null) {
+                mainId + (buildType.applicationIdSuffix ?: "")
+            } else {
+                null
+            }
+
+        return result
+    }
+
     /**
      * Generate BuildConfig.java if requested. Also look up if any BuildConfig is defined on the current build type,
      * product flavor or main project, and use them to generate any additional field (in that order to
      * respect the priorities). Return the generated file if it was generated, null otherwise.
      */
     fun maybeGenerateBuildConfig(project: Project, context: KobaltContext) : File? {
-        val buildConfigs = findBuildConfigs(project, context.variant)
+        val buildConfigs = findBuildConfigs(project, this)
 
         if (buildConfigs.size > 0) {
             val androidConfig = (Kobalt.findPlugin(AndroidPlugin.PLUGIN_NAME) as AndroidPlugin)
                     .configurationFor(project)
-            val pkg = androidConfig?.applicationId ?: project.packageName ?: project.group
+            val pkg = applicationId(androidConfig) ?: project.packageName ?: project.group
                     ?: throw KobaltException(
                     "packageName needs to be defined on the project in order to generate BuildConfig")
 
-            val code = project.projectInfo.generateBuildConfig(project, context, pkg, context.variant, buildConfigs)
-            val result = KFiles.makeDir(KFiles.generatedSourceDir(project, context.variant, "buildConfig"))
+            val code = project.projectInfo.generateBuildConfig(project, context, pkg, this, buildConfigs)
+            val result = KFiles.makeDir(KFiles.generatedSourceDir(project, this, "buildConfig"))
             // Make sure the generatedSourceDirectory doesn't contain the project.directory since
             // that directory will be added when trying to find recursively all the sources in it
             generatedSourceDirectory = File(result.relativeTo(File(project.directory)))
diff --git a/src/main/kotlin/com/beust/kobalt/api/ICompilerFlagContributor.kt b/src/main/kotlin/com/beust/kobalt/api/ICompilerFlagContributor.kt
index 87757868..13396d0e 100644
--- a/src/main/kotlin/com/beust/kobalt/api/ICompilerFlagContributor.kt
+++ b/src/main/kotlin/com/beust/kobalt/api/ICompilerFlagContributor.kt
@@ -4,5 +4,5 @@ package com.beust.kobalt.api
  * Plugins that add compiler flags.
  */
 interface ICompilerFlagContributor : IContributor {
-    fun flagsFor(project: Project, currentFlags: List<String>): List<String>
+    fun flagsFor(project: Project, context: KobaltContext, currentFlags: List<String>): List<String>
 }
diff --git a/src/main/kotlin/com/beust/kobalt/api/Project.kt b/src/main/kotlin/com/beust/kobalt/api/Project.kt
index 1cf16a00..43996ed3 100644
--- a/src/main/kotlin/com/beust/kobalt/api/Project.kt
+++ b/src/main/kotlin/com/beust/kobalt/api/Project.kt
@@ -181,6 +181,7 @@ interface IBuildConfig {
 }
 
 class ProductFlavorConfig(val name: String) : IBuildConfig {
+    var applicationId: String? = null
     override var buildConfig : BuildConfig? = BuildConfig()
 }
 
@@ -192,6 +193,7 @@ fun Project.productFlavor(name: String, init: ProductFlavorConfig.() -> Unit) =
 
 class BuildTypeConfig(val project: Project?, val name: String) : IBuildConfig {
     var minifyEnabled = false
+    var applicationIdSuffix: String? = null
     var proguardFile: String? = null
 
     fun getDefaultProguardFile(name: String) : String {
diff --git a/src/main/kotlin/com/beust/kobalt/internal/JvmCompiler.kt b/src/main/kotlin/com/beust/kobalt/internal/JvmCompiler.kt
index b6c3d1ff..a770ffc5 100644
--- a/src/main/kotlin/com/beust/kobalt/internal/JvmCompiler.kt
+++ b/src/main/kotlin/com/beust/kobalt/internal/JvmCompiler.kt
@@ -31,7 +31,7 @@ class JvmCompiler @Inject constructor(val dependencyManager: DependencyManager)
         // Plugins that add flags to the compiler
         val contributorFlags = if (project != null) {
             context.pluginInfo.compilerFlagContributors.flatMap {
-                it.flagsFor(project, info.compilerArgs)
+                it.flagsFor(project, context, info.compilerArgs)
             }
         } else {
             emptyList()
diff --git a/src/main/kotlin/com/beust/kobalt/internal/JvmCompilerPlugin.kt b/src/main/kotlin/com/beust/kobalt/internal/JvmCompilerPlugin.kt
index 70880215..cd4d5ae4 100644
--- a/src/main/kotlin/com/beust/kobalt/internal/JvmCompilerPlugin.kt
+++ b/src/main/kotlin/com/beust/kobalt/internal/JvmCompilerPlugin.kt
@@ -179,7 +179,8 @@ abstract class JvmCompilerPlugin @Inject constructor(
                 dependencyManager.dependencies(project, context, projects)
 
         val projectDirectory = File(project.directory)
-        val buildDirectory = File(project.classesDir(context))
+        val buildDirectory = if (isTest) KFiles.makeOutputTestDir(project)
+                else File(project.classesDir(context))
         buildDirectory.mkdirs()
 
         val initialSourceDirectories = arrayListOf<File>()
@@ -199,7 +200,7 @@ abstract class JvmCompilerPlugin @Inject constructor(
                 context.pluginInfo.sourceDirectoriesInterceptors.fold(initialSourceDirectories.toList(),
                         { sd, interceptor -> interceptor.intercept(project, context, sd) })
             }.filter {
-                it.exists()
+                File(project.directory, it.path).exists()
             }
 
         // Now that we have the final list of source dirs, find source files in them
diff --git a/src/main/kotlin/com/beust/kobalt/maven/RepoFinder.kt b/src/main/kotlin/com/beust/kobalt/maven/RepoFinder.kt
index 666c2f9e..5c3e81f9 100644
--- a/src/main/kotlin/com/beust/kobalt/maven/RepoFinder.kt
+++ b/src/main/kotlin/com/beust/kobalt/maven/RepoFinder.kt
@@ -49,7 +49,7 @@ public class RepoFinder @Inject constructor(val executors: KobaltExecutors) {
             for (i in 0..Kobalt.repos.size - 1) {
                 try {
                     val result = cs.take().get(2000, TimeUnit.MILLISECONDS)
-                    log(2, "Result for repo #$i: $result")
+                    log(2, "  Result for repo #$i: $result")
                     if (result.found) {
                         log(2, "Located $id in ${result.hostConfig.url}")
                         return result
@@ -70,7 +70,7 @@ public class RepoFinder @Inject constructor(val executors: KobaltExecutors) {
     inner class RepoFinderCallable(val id: String, val repo: HostConfig) : Callable<RepoResult> {
         override fun call(): RepoResult {
             val repoUrl = repo.url
-            log(2, "Checking $repoUrl for $id")
+            log(2, "  Checking $repoUrl for $id")
 
             val mavenId = MavenId(id)
             val groupId = mavenId.groupId
diff --git a/src/main/kotlin/com/beust/kobalt/plugin/android/AndroidBuild.kt b/src/main/kotlin/com/beust/kobalt/plugin/android/AndroidBuild.kt
index 1b07e960..a591613c 100644
--- a/src/main/kotlin/com/beust/kobalt/plugin/android/AndroidBuild.kt
+++ b/src/main/kotlin/com/beust/kobalt/plugin/android/AndroidBuild.kt
@@ -116,18 +116,17 @@ class AndroidBuild {
         //
         // Manifest
         //
-        val mainManifest = File("src/main/AndroidManifest.xml")
-
-        val appInfo = AppInfo(mainManifest, config)
-        val manifestOverlays = listOf(
-                File("src/${variant.productFlavor.name}/AndroidManifest.xml"),
-                File("src/${variant.buildType.name}/AndroidManifest.xml")).filter {
-                    it.exists()
-                }
+        val manifestOverlays = variant.allDirectories(project).map {
+                File("src/$it/AndroidManifest.xml")
+            }.filter {
+                it.exists()
+            }
         val libraries = listOf<ManifestDependency>()
         val outManifest = AndroidFiles.mergedManifest(project, variant)
         val outAaptSafeManifestLocation = KFiles.joinDir(project.directory, project.buildDirectory, "generatedSafeAapt")
         val reportFile = File(KFiles.joinDir(project.directory, project.buildDirectory, "manifest-merger-report.txt"))
+        val mainManifest = File("src/main/AndroidManifest.xml")
+        val appInfo = AppInfo(mainManifest, config)
         androidBuilder.mergeManifests(mainManifest, manifestOverlays, libraries,
                 null /* package override */,
                 appInfo.versionCode,
diff --git a/src/main/kotlin/com/beust/kobalt/plugin/android/AndroidFiles.kt b/src/main/kotlin/com/beust/kobalt/plugin/android/AndroidFiles.kt
index 3d504e6a..11e864f3 100644
--- a/src/main/kotlin/com/beust/kobalt/plugin/android/AndroidFiles.kt
+++ b/src/main/kotlin/com/beust/kobalt/plugin/android/AndroidFiles.kt
@@ -12,9 +12,8 @@ class AndroidFiles {
         fun intermediates(project: Project) = KFiles.joinDir(project.directory, project.buildDirectory,
                 "intermediates")
 
-        fun manifest(project: Project, context: KobaltContext) : String {
-            return KFiles.joinDir(project.directory, "src/main", "AndroidManifest.xml")
-        }
+        fun manifest(project: Project, context: KobaltContext) =
+                KFiles.joinDir(project.directory, "src", "main", "AndroidManifest.xml")
 
         fun mergedManifest(project: Project, variant: Variant) : String {
             val dir = KFiles.joinAndMakeDir(intermediates(project), "manifests", "full", variant.toIntermediateDir())
diff --git a/src/main/kotlin/com/beust/kobalt/plugin/android/AndroidPlugin.kt b/src/main/kotlin/com/beust/kobalt/plugin/android/AndroidPlugin.kt
index 9d61a956..92ccda09 100644
--- a/src/main/kotlin/com/beust/kobalt/plugin/android/AndroidPlugin.kt
+++ b/src/main/kotlin/com/beust/kobalt/plugin/android/AndroidPlugin.kt
@@ -164,7 +164,7 @@ public class AndroidPlugin @Inject constructor(val javaCompiler: JavaCompiler, v
      * Make sure we compile and generate 1.6 sources unless the build file defined those (which can
      * happen if the developer is using RetroLambda for example).
      */
-    override fun flagsFor(project: Project, currentFlags: List<String>) : List<String> {
+    override fun flagsFor(project: Project, context: KobaltContext, currentFlags: List<String>) : List<String> {
         if (isAndroid(project)) {
             var found = currentFlags.any { it == "-source" || it == "-target" }
             val result = arrayListOf<String>().apply { addAll(currentFlags) }
@@ -218,7 +218,7 @@ public class AndroidPlugin @Inject constructor(val javaCompiler: JavaCompiler, v
             project.compileDependencies).map {
                 it.jarFile.get().path
             }.filterNot {
-                it.contains("android.jar") || it.endsWith(".aar") || it.contains("com.android.support")
+                it.contains("android.jar") || it.endsWith(".aar")
                     || it.contains("retrolambda")
             }.toHashSet().toTypedArray()
 
@@ -367,13 +367,14 @@ public class AndroidPlugin @Inject constructor(val javaCompiler: JavaCompiler, v
     }
 
     override fun run(project: Project, context: KobaltContext, classpath: List<IClasspathDependency>): TaskResult {
-        val manifest = AndroidFiles.manifest(project, context)
-        FileInputStream(File(manifest)).use { ins ->
-            // adb shell am start -n com.package.name/com.package.name.ActivityName
-            val manifest = AndroidManifest(ins)
-            RunCommand(adb(project)).useErrorStreamAsErrorIndicator(false).run(args = listOf(
-                    "shell", "am", "start", "-n", manifest.pkg + "/" + manifest.mainActivity))
-            return TaskResult()
+        AndroidFiles.mergedManifest(project, context.variant).let { manifestPath ->
+            FileInputStream(File(manifestPath)).use { ins ->
+                // adb shell am start -n com.package.name/com.package.name.ActivityName
+                val manifest = AndroidManifest(ins)
+                RunCommand(adb(project)).useErrorStreamAsErrorIndicator(false).run(args = listOf(
+                        "shell", "am", "start", "-n", manifest.pkg + "/" + manifest.mainActivity))
+                return TaskResult()
+            }
         }
     }
 
diff --git a/src/main/kotlin/com/beust/kobalt/plugin/apt/AptPlugin.kt b/src/main/kotlin/com/beust/kobalt/plugin/apt/AptPlugin.kt
index 27558895..7cf40947 100644
--- a/src/main/kotlin/com/beust/kobalt/plugin/apt/AptPlugin.kt
+++ b/src/main/kotlin/com/beust/kobalt/plugin/apt/AptPlugin.kt
@@ -19,14 +19,19 @@ import javax.inject.Singleton
 @Singleton
 public class AptPlugin @Inject constructor(val depFactory: DepFactory)
         : ConfigPlugin<AptConfig>(), ICompilerFlagContributor {
+
     companion object {
         const val PLUGIN_NAME = "Apt"
     }
 
     override val name = PLUGIN_NAME
 
+    private fun generated(project: Project, context: KobaltContext, outputDir: String) =
+            KFiles.joinAndMakeDir(project.directory, project.buildDirectory, outputDir,
+                    context.variant.toIntermediateDir())
+
     // ICompilerFlagContributor
-    override fun flagsFor(project: Project, currentFlags: List<String>) : List<String> {
+    override fun flagsFor(project: Project, context: KobaltContext, currentFlags: List<String>) : List<String> {
         val result = arrayListOf<String>()
         configurationFor(project)?.let { config ->
             aptDependencies[project.name]?.let { aptDependencies ->
@@ -44,9 +49,8 @@ public class AptPlugin @Inject constructor(val depFactory: DepFactory)
 
                 result.add("-processorpath")
                 result.add((dependencyJarFiles + dependencies).joinToString(":"))
-                val generated = KFiles.joinAndMakeDir(project.directory, project.buildDirectory, config.outputDir)
                 result.add("-s")
-                result.add(generated)
+                result.add(generated(project, context, config.outputDir))
             }
             log(2, "New flags from apt: " + result.joinToString(" "))
         }
diff --git a/src/main/kotlin/com/beust/kobalt/plugin/java/JavaCompiler.kt b/src/main/kotlin/com/beust/kobalt/plugin/java/JavaCompiler.kt
index e71c3cbe..42d8c3cf 100644
--- a/src/main/kotlin/com/beust/kobalt/plugin/java/JavaCompiler.kt
+++ b/src/main/kotlin/com/beust/kobalt/plugin/java/JavaCompiler.kt
@@ -9,12 +9,14 @@ import com.beust.kobalt.api.Project
 import com.beust.kobalt.internal.ICompilerAction
 import com.beust.kobalt.internal.JvmCompiler
 import com.beust.kobalt.misc.KFiles
-import com.beust.kobalt.misc.log
 import com.beust.kobalt.misc.warn
-import com.beust.kobalt.plugin.android.forward
 import com.google.inject.Inject
 import com.google.inject.Singleton
 import java.io.File
+import java.io.PrintWriter
+import javax.tools.DiagnosticCollector
+import javax.tools.JavaFileObject
+import javax.tools.ToolProvider
 
 @Singleton
 class JavaCompiler @Inject constructor(val jvmCompiler: JvmCompiler) {
@@ -25,31 +27,25 @@ class JavaCompiler @Inject constructor(val jvmCompiler: JvmCompiler) {
                 return TaskResult()
             }
 
-            info.outputDir.mkdirs()
-
             val allArgs = arrayListOf(
-                    executable.absolutePath,
                     "-d", KFiles.makeDir(info.directory!!, info.outputDir.path).path)
             if (info.dependencies.size > 0) {
                 allArgs.add("-classpath")
-                allArgs.add(info.dependencies.map {it.jarFile.get()}.joinToString(File.pathSeparator))
+                allArgs.add(info.dependencies.map { it.jarFile.get() }.joinToString(File.pathSeparator))
             }
             allArgs.addAll(info.compilerArgs)
-            allArgs.addAll(info.sourceFiles)
 
-            val pb = ProcessBuilder(allArgs)
-//            info.directory?.let {
-//                pb.directory(File(it))
-//            }
-            pb.inheritIO()
-            val line = allArgs.joinToString(" ")
-            log(1, "  Compiling ${info.sourceFiles.size} files")
-            log(2, "  Compiling ${line.forward()}")
-            val process = pb.start()
-            val errorCode = process.waitFor()
+            val compiler = ToolProvider.getSystemJavaCompiler()
+            val fileManager = compiler.getStandardFileManager(null, null, null)
+            val fileObjects = fileManager.getJavaFileObjectsFromFiles(info.sourceFiles.map { File(it) })
+            val dc = DiagnosticCollector<JavaFileObject>()
+            val classes = arrayListOf<String>()
+            val task = compiler.getTask(PrintWriter(System.out), fileManager, dc, allArgs, classes, fileObjects)
+            val result = task.call()
 
-            return if (errorCode == 0) TaskResult(true, "Compilation succeeded")
+            return if (result) TaskResult(true, "Compilation succeeded")
                 else TaskResult(false, "There were errors")
+
         }
     }
 
diff --git a/src/main/resources/kobalt.properties b/src/main/resources/kobalt.properties
index 58905964..ea6bd2cf 100644
--- a/src/main/resources/kobalt.properties
+++ b/src/main/resources/kobalt.properties
@@ -1 +1 @@
-kobalt.version=0.318
+kobalt.version=0.320