[2.x] fix: allow defining root project with extraProjects (#4976) (#8694)

When an AutoPlugin adds a project at the build root via extraProjects,
avoid creating a second root from the build definition so both do not
share the same target directory. Treat extraProjects root as 'root
already defined' and exclude the build-defined root from initialProjects
when both would be at the same base.

main/src/main/scala/sbt/internal/Load.scala

@@ -812,10 +812,17 @@ private[sbt] object Load {
           mkReporter,
         )
       }
+      val projectsFromBuildDef = defsScala.flatMap(b => projectsFromBuild(b, normBase))
+      val rootFromExtra =
+        buildLevelExtraProjects.filter(p => isRootPath(p.base, normBase))
       val initialProjects =
-        defsScala.flatMap(b => projectsFromBuild(b, normBase)) ++ buildLevelExtraProjects
-
-      val hasRootAlreadyDefined = defsScala.exists(_.rootProject.isDefined)
+        if rootFromExtra.nonEmpty then
+          projectsFromBuildDef.filterNot(p =>
+            isRootPath(p.base, normBase)
+          ) ++ buildLevelExtraProjects
+        else projectsFromBuildDef ++ buildLevelExtraProjects
+      val hasRootAlreadyDefined =
+        defsScala.exists(_.rootProject.isDefined) || rootFromExtra.nonEmpty
 
       val memoSettings = new mutable.HashMap[VirtualFile, LoadedSbtFile]
       def loadProjects(ps: Seq[Project], createRoot: Boolean) =
@@ -1086,11 +1093,9 @@ private[sbt] object Load {
       val DiscoveredProjects(rootOpt, discovered, files, extraFiles, generated) = discover(
         p.base
       )
-
-      // TODO: We assume here the project defined in a build.sbt WINS because the original was a
-      // phony.  However, we may want to 'merge' the two, or only do this if the original was a
-      // default generated project.
-      val root = rootOpt.getOrElse(p)
+      val root =
+        if p.projectOrigin == ProjectOrigin.ExtraProject && isRootPath(p.base, buildBase) then p
+        else rootOpt.getOrElse(p)
       val (finalRoot, projectLevelExtra) = processProject(root, files, extraFiles, true)
       val newProjects = rest ++ discovered ++ projectLevelExtra
       val newAcc = acc :+ finalRoot

sbt-app/src/sbt-test/project/extra-projects-root/build.sbt

@@ -0,0 +1,2 @@
+// Minimal build so the build definition contributes a root; the plugin's extraProjects
+// root (foo at file(".")) should win and be the only root (#4976).

sbt-app/src/sbt-test/project/extra-projects-root/project/RootFromExtraPlugin.scala

@@ -0,0 +1,19 @@
+/*
+ * sbt
+ * Copyright 2023, Scala center
+ * Copyright 2011 - 2022, Lightbend, Inc.
+ * Copyright 2008 - 2010, Mark Harrah
+ * Licensed under Apache License 2.0 (see LICENSE)
+ */
+
+import sbt._, Keys._
+
+/**
+ * Reproduces #4976 / Dale's use case: plugin defines the root project via extraProjects.
+ * Without the fix, loading fails with "Overlapping output directories" (build root + foo).
+ */
+object RootFromExtraPlugin extends AutoPlugin {
+  override def trigger = allRequirements
+  override def extraProjects: Seq[Project] =
+    Seq(Project("foo", file(".")).settings(name := "foo"))
+}

sbt-app/src/sbt-test/project/extra-projects-root/test

@@ -0,0 +1,6 @@
+# Root project is defined by plugin via extraProjects (#4976). Without the fix,
+# loading fails with "Overlapping output directories" (build root + foo).
+
+> compile
+
+> show name