diff --git a/idea/src/mill/idea/GenIdeaImpl.scala b/idea/src/mill/idea/GenIdeaImpl.scala
index dcde5b11c11..8e96dd72c0c 100755
--- a/idea/src/mill/idea/GenIdeaImpl.scala
+++ b/idea/src/mill/idea/GenIdeaImpl.scala
@@ -68,20 +68,19 @@ case class GenIdeaImpl(
       fetchMillModules: Boolean = true
   ): Seq[(os.SubPath, scala.xml.Node)] = {
 
-    val rootModules = evaluators.map { ev => (ev.rootModule, ev) }
-    val transitive: Seq[(BaseModule, Seq[Module], Evaluator)] = rootModules
-      .map { case (rootModule, ev) =>
-        (rootModule, JavaModuleUtils.transitiveModules(rootModule), ev)
+    val rootModules = evaluators.zipWithIndex.map { case (ev, idx) => (ev.rootModule, ev, idx) }
+    val transitive: Seq[(BaseModule, Seq[Module], Evaluator, Int)] = rootModules
+      .map { case (rootModule, ev, idx) =>
+        (rootModule, JavaModuleUtils.transitiveModules(rootModule), ev, idx)
       }
 
     val foundModules: Seq[(Segments, Module, Evaluator)] = transitive
-      .flatMap { case (rootModule0, otherModules, ev) =>
-        (Seq(rootModule0) ++ otherModules).collect {
+      .flatMap { case (rootMod, transModules, ev, idx) =>
+        transModules.collect {
           case m: Module =>
-            val segments: Seq[String] =
-              rootModule0.millSourcePath.relativeTo(workDir).segments ++
-                m.millModuleSegments.parts
-
+            val rootSegs = rootMod.millSourcePath.relativeTo(workDir).segments
+            val modSegs = m.millModuleSegments.parts
+            val segments: Seq[String] = rootSegs ++ modSegs
             (Segments(segments.map(Segment.Label)), m, ev)
         }
       }
@@ -93,7 +92,6 @@ case class GenIdeaImpl(
 
     lazy val modulesByEvaluator: Map[Evaluator, Seq[(Segments, JavaModule)]] = modules
       .groupMap { case (_, _, ev) => ev } { case (s, m, _) => (s, m) }
-//      .toSeq
 
 //    val modules: Seq[(Segments, JavaModule)] =
 //      rootModule.millInternal.segmentsToModules.values
@@ -458,10 +456,10 @@ case class GenIdeaImpl(
           modules.map { case (segments, mod, _) => moduleName(segments) }.sorted
         )
       ),
-      Tuple2(
-        os.sub / "mill_modules" / "mill-build.iml",
-        rootXmlTemplate(allBuildLibraries.flatMap(lib => libraryNames(lib)))
-      ),
+//      Tuple2(
+//        os.sub / "mill_modules" / "mill-build.iml",
+//        rootXmlTemplate(allBuildLibraries.flatMap(lib => libraryNames(lib)))
+//      ),
       Tuple2(
         os.sub / "scala_compiler.xml",
         scalaCompilerTemplate(compilerSettings)
@@ -698,10 +696,11 @@ case class GenIdeaImpl(
     <project version={"" + ideaConfigVersion}>
       <component name="ProjectModuleManager">
         <modules>
-          <module
-            fileurl="file://$PROJECT_DIR$/.idea/mill_modules/mill-build.iml"
-            filepath="$PROJECT_DIR$/.idea/mill_modules/mill-build.iml"
-          />
+          {
+//            <module
+//          fileurl="file://$PROJECT_DIR$/.idea/mill_modules/mill-build.iml"
+//          filepath="$PROJECT_DIR$/.idea/mill_modules/mill-build.iml"/>
+    }
           {
       for (selector <- selectors)
         yield {
diff --git a/integration/feature/gen-idea/repo/extended/build.sc b/integration/feature/gen-idea/repo/extended/build.sc
index e345f8d44cd..1f1e6cd14ae 100644
--- a/integration/feature/gen-idea/repo/extended/build.sc
+++ b/integration/feature/gen-idea/repo/extended/build.sc
@@ -1,4 +1,4 @@
-import $ivy.`org.scalameta::munit:0.7.29`
+import $meta._
 
 import mill._
 import mill.api.PathRef
diff --git a/integration/feature/gen-idea/repo/extended/idea/mill_modules/mill-build.iml b/integration/feature/gen-idea/repo/extended/idea/mill_modules/mill-build.iml
index 92beb65794b..f4900de873b 100644
--- a/integration/feature/gen-idea/repo/extended/idea/mill_modules/mill-build.iml
+++ b/integration/feature/gen-idea/repo/extended/idea/mill_modules/mill-build.iml
@@ -5,6 +5,9 @@
         <content url="file://$MODULE_DIR$/../../out/mill-build/generateScriptSources.dest">
             <sourceFolder url="file://$MODULE_DIR$/../../out/mill-build/generateScriptSources.dest" isTestSource="false" generated="true"/>
         </content>
+        <content url="file://$MODULE_DIR$/../../build.sc">
+            <sourceFolder url="file://$MODULE_DIR$/../../build.sc" isTestSource="false"/>
+        </content>
         <content url="file://$MODULE_DIR$/../../mill-build/src">
             <sourceFolder url="file://$MODULE_DIR$/../../mill-build/src" isTestSource="false"/>
         </content>
diff --git a/integration/feature/gen-idea/repo/extended/idea/mill_modules/mill-build.mill-build.iml b/integration/feature/gen-idea/repo/extended/idea/mill_modules/mill-build.mill-build.iml
new file mode 100644
index 00000000000..7ae9ae8ba5c
--- /dev/null
+++ b/integration/feature/gen-idea/repo/extended/idea/mill_modules/mill-build.mill-build.iml
@@ -0,0 +1,15 @@
+<module type="JAVA_MODULE" version="4">
+    <component name="NewModuleRootManager">
+        <output url="file://$MODULE_DIR$/../../out/mill-build/mill-build/ideaCompileOutput.dest/classes"/>
+        <exclude-output/>
+        <content url="file://$MODULE_DIR$/../../out/mill-build/mill-build/generateScriptSources.dest">
+            <sourceFolder url="file://$MODULE_DIR$/../../out/mill-build/mill-build/generateScriptSources.dest" isTestSource="false" generated="true"/>
+        </content>
+        <content url="file://$MODULE_DIR$/../../mill-build/build.sc">
+            <sourceFolder url="file://$MODULE_DIR$/../../mill-build/build.sc" isTestSource="false"/>
+        </content>
+        <orderEntry type="inheritedJdk"/>
+        <orderEntry type="sourceFolder" forTests="false"/>
+<!-- IGNORE -->
+    </component>
+</module>
\ No newline at end of file
diff --git a/integration/feature/gen-idea/repo/extended/idea/modules.xml b/integration/feature/gen-idea/repo/extended/idea/modules.xml
index 26ce642df26..68f06794a08 100644
--- a/integration/feature/gen-idea/repo/extended/idea/modules.xml
+++ b/integration/feature/gen-idea/repo/extended/idea/modules.xml
@@ -1,11 +1,11 @@
 <project version="4">
     <component name="ProjectModuleManager">
         <modules>
-            <module fileurl="file://$PROJECT_DIR$/.idea/mill_modules/mill-build.iml" filepath="$PROJECT_DIR$/.idea/mill_modules/mill-build.iml"/>
             <module fileurl="file://$PROJECT_DIR$/.idea/mill_modules/helloworld.iml" filepath="$PROJECT_DIR$/.idea/mill_modules/helloworld.iml"/>
             <module fileurl="file://$PROJECT_DIR$/.idea/mill_modules/helloworld.subscala3.iml" filepath="$PROJECT_DIR$/.idea/mill_modules/helloworld.subscala3.iml"/>
             <module fileurl="file://$PROJECT_DIR$/.idea/mill_modules/helloworld.test.iml" filepath="$PROJECT_DIR$/.idea/mill_modules/helloworld.test.iml"/>
             <module fileurl="file://$PROJECT_DIR$/.idea/mill_modules/mill-build.iml" filepath="$PROJECT_DIR$/.idea/mill_modules/mill-build.iml"/>
+            <module fileurl="file://$PROJECT_DIR$/.idea/mill_modules/mill-build.mill-build.iml" filepath="$PROJECT_DIR$/.idea/mill_modules/mill-build.mill-build.iml"/>
         </modules>
     </component>
 </project>
diff --git a/integration/feature/gen-idea/repo/extended/mill-build/build.sc b/integration/feature/gen-idea/repo/extended/mill-build/build.sc
new file mode 100644
index 00000000000..5927948a8cd
--- /dev/null
+++ b/integration/feature/gen-idea/repo/extended/mill-build/build.sc
@@ -0,0 +1,6 @@
+import mill._
+import mill.scalalib._
+
+object root extends MillBuildRootModule {
+  def ivyDeps = Agg(ivy"org.scalameta::munit:0.7.29")
+}
\ No newline at end of file
diff --git a/integration/feature/gen-idea/repo/hello-world/idea/mill_modules/mill-build.iml b/integration/feature/gen-idea/repo/hello-world/idea/mill_modules/mill-build.iml
index 92beb65794b..234a3233c87 100644
--- a/integration/feature/gen-idea/repo/hello-world/idea/mill_modules/mill-build.iml
+++ b/integration/feature/gen-idea/repo/hello-world/idea/mill_modules/mill-build.iml
@@ -5,11 +5,8 @@
         <content url="file://$MODULE_DIR$/../../out/mill-build/generateScriptSources.dest">
             <sourceFolder url="file://$MODULE_DIR$/../../out/mill-build/generateScriptSources.dest" isTestSource="false" generated="true"/>
         </content>
-        <content url="file://$MODULE_DIR$/../../mill-build/src">
-            <sourceFolder url="file://$MODULE_DIR$/../../mill-build/src" isTestSource="false"/>
-        </content>
-        <content url="file://$MODULE_DIR$/../../mill-build/resources">
-            <sourceFolder url="file://$MODULE_DIR$/../../mill-build/resources" type="java-resource"/>
+        <content url="file://$MODULE_DIR$/../../build.sc">
+            <sourceFolder url="file://$MODULE_DIR$/../../build.sc" isTestSource="false"/>
         </content>
         <orderEntry type="inheritedJdk"/>
         <orderEntry type="sourceFolder" forTests="false"/>
diff --git a/integration/feature/gen-idea/repo/hello-world/idea/modules.xml b/integration/feature/gen-idea/repo/hello-world/idea/modules.xml
index 069c7a398f4..cab10e5c482 100644
--- a/integration/feature/gen-idea/repo/hello-world/idea/modules.xml
+++ b/integration/feature/gen-idea/repo/hello-world/idea/modules.xml
@@ -1,7 +1,6 @@
 <project version="4">
     <component name="ProjectModuleManager">
         <modules>
-            <module fileurl="file://$PROJECT_DIR$/.idea/mill_modules/mill-build.iml" filepath="$PROJECT_DIR$/.idea/mill_modules/mill-build.iml"/>
             <module fileurl="file://$PROJECT_DIR$/.idea/mill_modules/helloworld.iml" filepath="$PROJECT_DIR$/.idea/mill_modules/helloworld.iml"/>
             <module fileurl="file://$PROJECT_DIR$/.idea/mill_modules/helloworld.test.iml" filepath="$PROJECT_DIR$/.idea/mill_modules/helloworld.test.iml"/>
             <module fileurl="file://$PROJECT_DIR$/.idea/mill_modules/mill-build.iml" filepath="$PROJECT_DIR$/.idea/mill_modules/mill-build.iml"/>
diff --git a/integration/feature/gen-idea/test/src/GenIdeaExtendedTests.scala b/integration/feature/gen-idea/test/src/GenIdeaExtendedTests.scala
index 7d37aabbacd..e6b2bcfcf1a 100644
--- a/integration/feature/gen-idea/test/src/GenIdeaExtendedTests.scala
+++ b/integration/feature/gen-idea/test/src/GenIdeaExtendedTests.scala
@@ -18,9 +18,10 @@ object GenIdeaExtendedTests extends IntegrationTestSuite {
 
       val checks = Seq(
         os.sub / "mill_modules" / "helloworld.iml",
-        os.sub / "mill_modules" / "helloworld.test.iml",
         os.sub / "mill_modules" / "helloworld.subscala3.iml",
+        os.sub / "mill_modules" / "helloworld.test.iml",
         os.sub / "mill_modules" / "mill-build.iml",
+        os.sub / "mill_modules" / "mill-build.mill-build.iml",
         os.sub / "libraries" / s"scala_library_${scalaVersionLibPart}_jar.xml",
         // NOTE: on IntelliJ Scala Plugin side there is a cosmetic issue: scala suffix is added even for Java libraries (notice `_2_13` suffix)
         // In future it might be fixed and `GenIdea` will need to be updated
diff --git a/runner/src/mill/runner/FileImportGraph.scala b/runner/src/mill/runner/FileImportGraph.scala
index d5b041d90ed..cc8f87964e1 100644
--- a/runner/src/mill/runner/FileImportGraph.scala
+++ b/runner/src/mill/runner/FileImportGraph.scala
@@ -4,6 +4,15 @@ import mill.api.internal
 import scala.reflect.NameTransformer.encode
 import scala.collection.mutable
 
+/**
+ *
+ * @param seenScripts
+ * @param repos
+ * @param ivyDeps
+ * @param importGraphEdges
+ * @param errors
+ * @param millImport If `true`, a meta-build is enabled
+ */
 @internal
 case class FileImportGraph(
     seenScripts: Map[os.Path, String],
diff --git a/runner/src/mill/runner/MillBuildRootModule.scala b/runner/src/mill/runner/MillBuildRootModule.scala
index 25adc79fe85..3ba45986802 100644
--- a/runner/src/mill/runner/MillBuildRootModule.scala
+++ b/runner/src/mill/runner/MillBuildRootModule.scala
@@ -7,11 +7,9 @@ import mill.define.{Caller, Discover, Target, Task}
 import mill.scalalib.{BoundDep, Dep, DepSyntax, Lib, ScalaModule}
 import mill.util.CoursierSupport
 import mill.util.Util.millProjectModule
-import mill.scalalib.api.Versions
-import os.{Path, rel}
+import mill.scalalib.api.{CompilationResult, Versions}
 import pprint.Util.literalize
 import FileImportGraph.backtickWrap
-import mill.codesig.CodeSig
 import mill.main.BuildInfo
 
 import scala.collection.immutable.SortedMap
@@ -61,20 +59,26 @@ class MillBuildRootModule()(implicit
 
   override def scalaVersion: T[String] = "2.13.10"
 
-  def scriptSources = T.sources {
-    MillBuildRootModule
-      .parseBuildFiles(millBuildRootModuleInfo)
-      .seenScripts
-      .keys
-      .map(PathRef(_))
-      .toSeq
+  def scriptSources = T {
+//    MillBuildRootModule
+//      .parseBuildFiles(millBuildRootModuleInfo)
+//      .seenScripts
+//      .keys
+//      .map(PathRef(_))
+//      .toSeq
+    parseBuildFiles().seenScripts.keys.map(PathRef(_)).toSeq
   }
 
-  def parseBuildFiles = T {
-    scriptSources()
+  def parseBuildFiles: T[FileImportGraph] = T.input {
+//    scriptSources()
     MillBuildRootModule.parseBuildFiles(millBuildRootModuleInfo)
   }
 
+//  override def compile: T[CompilationResult] = T {
+//    println("compile")
+//    super.compile()
+//  }
+
   override def repositoriesTask: Task[Seq[Repository]] = {
     val importedRepos = T.task {
       val repos = parseBuildFiles().repos.map { case (repo, srcFile) =>
@@ -139,7 +143,7 @@ class MillBuildRootModule()(implicit
     }
   }
 
-  def scriptImportGraph: T[Map[Path, (Int, Seq[Path])]] = T {
+  def scriptImportGraph: T[Map[os.Path, (Int, Seq[os.Path])]] = T {
     parseBuildFiles()
       .importGraphEdges
       .map { case (path, imports) =>
@@ -211,8 +215,26 @@ class MillBuildRootModule()(implicit
     result
   }
 
+  override def sources: T[Seq[PathRef]] = T {
+//    Lib.findSourceFiles(allSources(), Seq("scala", "java", "sc")).map(PathRef(_))
+//    val files = parseBuildFiles().seenScripts.keys
+//    println(s"sources: ${files.map(_.relativeTo(T.workspace))}")
+//    files.map(PathRef(_)).toSeq
+    scriptSources() ++ {
+      if (parseBuildFiles().millImport) super.sources()
+      else Seq.empty[PathRef]
+    }
+  }
+
+  override def resources: T[Seq[PathRef]] = T {
+    if (parseBuildFiles().millImport) super.resources()
+    else Seq.empty[PathRef]
+  }
+
   override def allSourceFiles: T[Seq[PathRef]] = T {
-    Lib.findSourceFiles(allSources(), Seq("scala", "java", "sc")).map(PathRef(_))
+    // We ignore the sc files, as we generate scala files for them
+    // Lib.findSourceFiles(allSources(), Seq("scala", "java", "sc")).map(PathRef(_))
+    Lib.findSourceFiles(allSources(), Seq("scala", "java")).map(PathRef(_))
   }
 
   def enclosingClasspath = T.sources {
@@ -277,7 +299,7 @@ object MillBuildRootModule {
       cliImports: Seq[String]
   )
 
-  def parseBuildFiles(millBuildRootModuleInfo: MillBuildRootModule.Info) = {
+  def parseBuildFiles(millBuildRootModuleInfo: MillBuildRootModule.Info): FileImportGraph = {
     FileImportGraph.parseBuildFiles(
       millBuildRootModuleInfo.topLevelProjectRoot,
       millBuildRootModuleInfo.projectRoot / os.up
@@ -295,7 +317,13 @@ object MillBuildRootModule {
   ): Unit = {
     for (scriptSource <- scriptSources) {
       val relative = scriptSource.path.relativeTo(base)
-      val dest = targetDest / FileImportGraph.fileImportToSegments(base, scriptSource.path, false)
+      val dest0 = targetDest / FileImportGraph.fileImportToSegments(base, scriptSource.path, false)
+      val dest =
+        if (dest0.ext == "sc") {
+          dest0 / os.up / (dest0.baseName + ".scala")
+        } else {
+          dest0
+        }
 
       val newSource = MillBuildRootModule.top(
         relative,