diff --git a/tapeout/src/main/scala/transforms/Generate.scala b/tapeout/src/main/scala/transforms/Generate.scala
index 2c68a4e8..f9b3e8dc 100644
--- a/tapeout/src/main/scala/transforms/Generate.scala
+++ b/tapeout/src/main/scala/transforms/Generate.scala
@@ -15,10 +15,10 @@ object AllModules {
   def add(module: String) = {
     modules = modules | Set(module)
   }
-  def rename(module: String) = {
+  def rename(module: String, suffix: String = "_inTestHarness") = {
     var new_name = module
     while (modules.contains(new_name))
-      new_name = new_name + "_inTestHarness"
+      new_name = new_name + suffix
     new_name
   }
 }
@@ -28,17 +28,6 @@ trait HasTapeoutOptions { self: ExecutionOptionsManager with HasFirrtlOptions =>
 
   parser.note("tapeout options")
 
-  parser.opt[String]("top-o")
-    .abbr("tto")
-    .valueName("<top-output>")
-    .foreach { x =>
-      tapeoutOptions = tapeoutOptions.copy(
-        topOutput = Some(x)
-      )
-    }.text {
-      "use this to generate top at <top-output>"
-    }
-
   parser.opt[String]("harness-o")
     .abbr("tho")
     .valueName("<harness-output>")
@@ -72,173 +61,87 @@ trait HasTapeoutOptions { self: ExecutionOptionsManager with HasFirrtlOptions =>
       "use this to set harnessTop"
     }
 
-  parser.opt[String]("list-clocks")
-    .abbr("tlc")
-    .valueName("<clocks>")
-    .foreach { x =>
-      tapeoutOptions = tapeoutOptions.copy(
-        listClocks = Some(x)
-      )
-    }.text {
-      "use this to list <clocks>"
-    }
-
   parser.note("")
 }
 
 case class TapeoutOptions(
-  input: Option[String] = None,
-  output: Option[String] = None,
-  topOutput: Option[String] = None,
   harnessOutput: Option[String] = None,
-  annoFile: Option[String] = None,
   synTop: Option[String] = None,
-  harnessTop: Option[String] = None,
-  seqMemFlags: Option[String] = Some("-o:unused.confg"),
-  listClocks: Option[String] = Some("-o:unused.clocks")
+  harnessTop: Option[String] = None
 ) extends LazyLogging
 
 // Requires two phases, one to collect modules below synTop in the hierarchy
 // and a second to remove those modules to generate the test harness
 sealed trait GenerateTopAndHarnessApp extends LazyLogging { this: App =>
-  lazy val optionsManager = {
+  def getOptionsManager = {
     val optionsManager = new ExecutionOptionsManager("tapeout") with HasFirrtlOptions with HasTapeoutOptions
     if (!optionsManager.parse(args)) {
       throw new Exception("Error parsing options!")
     }
     optionsManager
   }
-  lazy val options = optionsManager.tapeoutOptions
-  lazy val input = options.input
-  lazy val output = options.output
-  lazy val topOutput = options.topOutput
-  lazy val harnessOutput = options.harnessOutput
-  lazy val annoFile = options.annoFile
-  lazy val synTop = options.synTop
-  lazy val harnessTop = options.harnessTop
-  lazy val seqMemFlags = options.seqMemFlags
-  lazy val listClocks = options.listClocks
+  lazy val optionsManager = getOptionsManager
+  lazy val tapeoutOptions = optionsManager.tapeoutOptions
+  // Tapeout options
+  lazy val harnessOutput = tapeoutOptions.harnessOutput
+  lazy val synTop = tapeoutOptions.synTop
+  lazy val harnessTop = tapeoutOptions.harnessTop
 
-  private def getFirstPhasePasses(top: Boolean, harness: Boolean): Seq[Transform] = {
-    val pre = Seq(
+  lazy val firrtlOptions = optionsManager.firrtlOptions
+  // FIRRTL options
+  lazy val annoFiles = firrtlOptions.annotationFileNames
+
+  private def getFirstPhasePasses: Seq[Transform] = {
+    Seq(
       new ReParentCircuit(synTop.get),
+      new RemoveUnusedModules
     )
-
-    val enumerate = if (harness) { Seq(
-      new EnumerateModules( { m => if (m.name != options.harnessTop.get && m.name != options.synTop.get) { AllModules.add(m.name) } } ),
-    ) } else Seq()
-
-    val post = if (top) { Seq(
-      new RemoveUnusedModules,
-      new passes.memlib.InferReadWrite(),
-      new passes.clocklist.ClockListTransform()
-    ) } else Seq()
-
-    pre ++ enumerate ++ post
-  }
-
-  private def getFirstPhaseAnnotations(top: Boolean): AnnotationSeq = {
-    if (top) {
-      //Load annotations from file
-      val annotationArray: Seq[Annotation] = annoFile match {
-        case None => Array[Annotation]()
-        case Some(fileName) => {
-          val annotations = new File(fileName)
-          if(annotations.exists) {
-            val annotationsYaml = io.Source.fromFile(annotations).getLines().mkString("\n")
-            Seq(AnnotationUtils.fromYaml(annotationsYaml)) // TODO
-          } else {
-            Seq[Annotation]()
-          }
-        }
-      }
-      // add new annotations
-      AnnotationSeq(Seq(
-        passes.memlib.InferReadWriteAnnotation,
-        passes.clocklist.ClockListAnnotation.parse(
-          s"-c:${synTop.get}:-m:${synTop.get}:${listClocks.get}"
-        ),
-        passes.memlib.ReplSeqMemAnnotation.parse(
-          s"-c:${synTop.get}:${seqMemFlags.get}"
-        )
-      ) ++ annotationArray)
-    } else { AnnotationSeq(Seq.empty) }
   }
 
   private def getSecondPhasePasses: Seq[Transform] = {
-    // always the same for now
     Seq(
       new ConvertToExtMod((m) => m.name == synTop.get),
-      new RenameModulesAndInstances((m) => AllModules.rename(m)),
-      // new RemoveUnusedModules,
+      new EnumerateModules( { m => if (m.name != tapeoutOptions.harnessTop.get && m.name != tapeoutOptions.synTop.get) { AllModules.add(m.name) } } ),
+      new RenameModulesAndInstances((m) => AllModules.rename(m, "_in" + harnessTop.get)),
+      new RemoveUnusedModules
     )
   }
 
-  // always the same for now
-  private def getSecondPhaseAnnotations: AnnotationSeq = AnnotationSeq(Seq.empty)
-
   // Top Generation
-  protected def firstPhase(top: Boolean, harness: Boolean): Unit = {
-    require(top || harness, "Must specify either top or harness")
+  protected def firstPhase: Unit = {
 
-    val firrtlOptions = optionsManager.firrtlOptions
-    optionsManager.firrtlOptions = firrtlOptions.copy(
-      annotations = firrtlOptions.annotations ++ getFirstPhaseAnnotations(top)
+    val firstPhaseOptions = getOptionsManager
+    firstPhaseOptions.firrtlOptions = firstPhaseOptions.firrtlOptions.copy(
+      customTransforms = firrtlOptions.customTransforms ++ getFirstPhasePasses
     )
 
-    optionsManager.firrtlOptions = firrtlOptions.copy(
-      customTransforms = firrtlOptions.customTransforms ++ getFirstPhasePasses(top, harness)
-    )
+    firrtl.Driver.execute(firstPhaseOptions)
   }
 
   // Harness Generation
   protected def secondPhase: Unit = {
-    val firrtlOptions = optionsManager.firrtlOptions
-    optionsManager.firrtlOptions = firrtlOptions.copy(
-      annotations = firrtlOptions.annotations ++ getSecondPhaseAnnotations
+    val secondPhaseOptions = getOptionsManager
+    secondPhaseOptions.firrtlOptions = secondPhaseOptions.firrtlOptions.copy(
+      outputFileNameOverride = harnessOutput.get,
+      customTransforms = getSecondPhasePasses
     )
 
-    optionsManager.firrtlOptions = firrtlOptions.copy(
-      customTransforms = firrtlOptions.customTransforms ++ getSecondPhasePasses
-    )
-  }
-
-  protected def execute: Unit = {
-    firrtl.Driver.execute(optionsManager)
+    firrtl.Driver.execute(secondPhaseOptions)
   }
 }
 
 object GenerateTop extends App with GenerateTopAndHarnessApp {
-  // warn about unused options
-  harnessOutput.foreach(n => logger.warn(s"Not using harness output filename $n since you asked for just a top-level output."))
-  topOutput.foreach(
-    n => logger.warn(s"Not using generic output filename $n since you asked for just a top-level output and also specified a generic output."))
   // Only need a single phase to generate the top module
-  firstPhase(top = true, harness = false)
-  execute
+  firstPhase
 }
 
 object GenerateHarness extends App with GenerateTopAndHarnessApp {
-  // warn about unused options
-  topOutput.foreach(n => logger.warn(s"Not using top-level output filename $n since you asked for just a test harness."))
-  annoFile.foreach(n => logger.warn(s"Not using annotations file $n since you asked for just a test harness."))
-  seqMemFlags.filter(_ != "-o:unused.confg").foreach {
-    n => logger.warn(s"Not using SeqMem flags $n since you asked for just a test harness.") }
-  listClocks.filter(_ != "-o:unused.clocks").foreach {
-    n => logger.warn(s"Not using clocks list $n since you asked for just a test harness.") }
-  harnessOutput.foreach(
-    n => logger.warn(s"Not using generic output filename $n since you asked for just a test harness and also specified a generic output."))
   // Do minimal work for the first phase to generate test harness
-  firstPhase(top = false, harness = true)
   secondPhase
-  execute
 }
 
 object GenerateTopAndHarness extends App with GenerateTopAndHarnessApp {
-  // warn about unused options
-  output.foreach(n => logger.warn(s"Not using generic output filename $n since you asked for both a top-level output and a test harness."))
   // Do everything, top and harness generation
-  firstPhase(top = true, harness = true)
+  firstPhase
   secondPhase
-  execute
 }