diff --git a/src/scala/scripts/PBGenerateRequest.scala b/src/scala/scripts/PBGenerateRequest.scala
index a35d03c31..2b1a9660a 100644
--- a/src/scala/scripts/PBGenerateRequest.scala
+++ b/src/scala/scripts/PBGenerateRequest.scala
@@ -6,16 +6,44 @@ case class PBGenerateRequest(jarOutput: String, scalaPBOutput: Path, scalaPBArgs
 
 object PBGenerateRequest {
 
-  def from(args: java.util.List[String]): PBGenerateRequest = {
+  // If there is a virtual import in the path, then
+  // the path under there is pretty friendly already to protoc
+  def stripToVirtual(e: String): String = {
+    val v = "/_virtual_imports/"
+    val idx = e.indexOf(v)
+    if(idx >= 0) {
+      e.drop(idx + v.size)
+    } else e
+  }
+
+  def from(tmpDir: Path)(args: java.util.List[String]): PBGenerateRequest = {
     val jarOutput = args.get(0)
     val protoFiles = args.get(4).split(':')
-    val includedProto = args.get(1).drop(1).split(':').distinct.map { e =>
-      val p = e.split(',')
-      // If its an empty string then it means we are local to the current repo for the key, no op
-      (Some(p(0)).filter(_.nonEmpty), p(1))
-    }.collect {
-      // if the to compile files contains this absolute path then we are compiling it and shoudln't try move it around(duplicate files.)
-      case (Some(k), v) if !protoFiles.contains(v) => (Paths.get(k), Paths.get(v))
+    val protoFilesToBuild = protoFiles.map { e => s"${tmpDir.toFile.toString}/${stripToVirtual(e)}"}
+
+    val includedProtoSplit: List[(String, String)] = args.get(1).drop(1).split(':').map { e =>
+      val arr = e.split(',')
+      (arr(0), arr(1))
+    }.toList
+    val includedProto: List[(Path, Path)] = (includedProtoSplit ++ protoFiles.toList.map { e => ("", e)}).distinct.map { case (repoPath, protoPath) =>
+      // repoPath shoudl refer to the external repo root. If there is _virtual_imports this will
+      // be in here too.
+      //
+      // If virtual imports are present we are going to prefer that for calculating our target
+      // path. If not we will use relative to the external repo base.
+      // if not that, just use thhe path we have.
+
+      if(protoPath.contains("_virtual_imports")) {
+        (Paths.get(protoPath), Paths.get(stripToVirtual(protoPath)))
+      } else if (repoPath.nonEmpty) {
+        // We have a repo specified
+        // if the repo path and the file path are the same, no-op
+        // otherwise get a relative path.
+        val relativePath: Path = if(repoPath == protoPath) Paths.get(protoPath) else Paths.get(repoPath).relativize(Paths.get(protoPath))
+        (Paths.get(protoPath), relativePath)
+      } else {
+        (Paths.get(protoPath), Paths.get(protoPath))
+      }
     }.toList
 
     val flagOpt = args.get(2) match {
@@ -27,7 +55,7 @@ object PBGenerateRequest {
       case "-" => Nil
       case s if s.charAt(0) == '-' => s.tail.split(':').toList //drop padding character
       case other => sys.error(s"expected a padding character of - (dash), but found: $other")
-    }) ++ List(".")
+    }) ++ List("")
 
     val tmp = Paths.get(Option(System.getProperty("java.io.tmpdir")).getOrElse("/tmp"))
     val scalaPBOutput = Files.createTempDirectory(tmp, "bazelscalapb")
@@ -43,7 +71,8 @@ object PBGenerateRequest {
     }.toList
 
 
-    val scalaPBArgs = outputSettings ::: (padWithProtoPathPrefix(transitiveProtoPaths) ++ protoFiles)
+    val scalaPBArgs = outputSettings ::: (padWithProtoPathPrefix(tmpDir)(transitiveProtoPaths) ++ protoFilesToBuild)
+
     val protoc = Paths.get(args.get(5))
 
     val extraJars = args.get(7).drop(1).split(':').filter(_.nonEmpty).distinct.map {e => Paths.get(e)}.toList
@@ -51,7 +80,7 @@ object PBGenerateRequest {
     new PBGenerateRequest(jarOutput, scalaPBOutput, scalaPBArgs, includedProto, protoc, namedGenerators, extraJars)
   }
 
-  private def padWithProtoPathPrefix(transitiveProtoPathFlags: List[String]) =
-    transitiveProtoPathFlags.map("--proto_path="+_)
+  private def padWithProtoPathPrefix(tmpDir: Path)(transitiveProtoPathFlags: List[String]) =
+    transitiveProtoPathFlags.map(stripToVirtual).map(s"--proto_path=${tmpDir.toFile.toString}/"+_).map(_.stripSuffix("."))
 
 }
diff --git a/src/scala/scripts/ScalaPBGenerator.scala b/src/scala/scripts/ScalaPBGenerator.scala
index 5fdaa8937..ffa749c38 100644
--- a/src/scala/scripts/ScalaPBGenerator.scala
+++ b/src/scala/scripts/ScalaPBGenerator.scala
@@ -34,15 +34,15 @@ object ScalaPBWorker extends GenericWorker(new ScalaPBGenerator) {
 }
 
 class ScalaPBGenerator extends Processor {
-  def setupIncludedProto(includedProto: List[(Path, Path)]): Unit = {
-    includedProto.foreach { case (root, fullPath) =>
-      require(fullPath.toFile.exists, s"Path $fullPath does not exist, which it should as a dependency of this rule")
-      val relativePath = root.relativize(fullPath)
+  def setupIncludedProto(tmpRoot: Path, includedProto: List[(Path, Path)]): Unit = {
+    includedProto.foreach { case (srcPath, relativeTargetPath) =>
+      require(srcPath.toFile.exists, s"Path $srcPath does not exist, which it should as a dependency of this rule")
+      val targetPath = tmpRoot.resolve(relativeTargetPath)
 
-      relativePath.toFile.getParentFile.mkdirs
-      Try(Files.copy(fullPath, relativePath)) match {
+      targetPath.toFile.getParentFile.mkdirs
+      Try(Files.copy(srcPath, targetPath)) match {
         case Failure(err: FileAlreadyExistsException) =>
-          Console.println(s"File already exists, skipping: ${err.getMessage}")
+          Console.println(s"File already exists, skipping copy from $srcPath to $targetPath: ${err.getMessage}")
         case Failure(err) => throw err
         case _ => ()
       }
@@ -55,8 +55,10 @@ class ScalaPBGenerator extends Processor {
     }
 
   def processRequest(args: java.util.List[String]) {
-    val extractRequestResult = PBGenerateRequest.from(args)
-    setupIncludedProto(extractRequestResult.includedProto)
+    val tmpRoot = Files.createTempDirectory("proto_builder")
+
+    val extractRequestResult = PBGenerateRequest.from(tmpRoot)(args)
+    setupIncludedProto(tmpRoot, extractRequestResult.includedProto)
 
     val extraClassesClassLoader = new URLClassLoader(extractRequestResult.extraJars.map { e =>
       val f = e.toFile
@@ -89,10 +91,21 @@ class ScalaPBGenerator extends Processor {
         }
         JarCreator.buildJar(Array(extractRequestResult.jarOutput, extractRequestResult.scalaPBOutput.toString))
     } finally {
+      deleteDir(tmpRoot)
       deleteDir(extractRequestResult.scalaPBOutput)
     }
   }
 
-  protected def exec(protoc: Path): Seq[String] => Int = (args: Seq[String]) =>
-    new ProcessBuilder(protoc.toString +: args: _*).inheritIO().start().waitFor()
+  protected def exec(protoc: Path): Seq[String] => Int = (args: Seq[String]) => {
+    val tmpFile = Files.createTempFile("stdout", "log")
+    try {
+      val ret = new ProcessBuilder(protoc.toString +: args: _*).redirectErrorStream(true).redirectOutput(ProcessBuilder.Redirect.to(tmpFile.toFile)).start().waitFor()
+      Try {
+        scala.io.Source.fromFile(tmpFile.toFile).getLines.foreach{System.out.println}
+      }
+      ret
+    } finally {
+      tmpFile.toFile.delete
+    }
+  }
 }