Fix setting loading

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

@@ -1098,7 +1098,7 @@ private[sbt] object Load {
       // 3. Use AddSettings instance to order all Setting[_]s appropriately
       val allSettings = {
         // TODO - This mechanism of applying settings could be off... It's in two places now...
-        lazy val defaultSbtFiles = configurationSources(p.base)
+        lazy val defaultSbtFiles = configurationSources(p.base.getCanonicalFile())
           .map(_.getAbsoluteFile().toPath())
           .map(converter.toVirtualFile)
         lazy val sbtFiles: Seq[VirtualFile] = defaultSbtFiles ++ extraSbtFiles

sbt-app/src/sbt-test/actions/cross-advanced/build.sbt

@@ -2,6 +2,8 @@ lazy val check = taskKey[Unit]("")
 lazy val compile2 = taskKey[Unit]("")
 lazy val scala212 = "2.12.17"
 
+ThisBuild / scalaVersion := scala212
+
 lazy val root = (project in file("."))
   .aggregate(foo, bar, client)
   .settings(
@@ -13,7 +15,6 @@ lazy val foo = project
   .settings(
     crossScalaVersions := Seq(scala212, "2.13.1"),
     libraryDependencies += "org.scalatest" %% "scalatest" % "3.1.0",
-
     check := {
       // This tests that +check will respect bar's crossScalaVersions and not switch
       val x = (LocalProject("bar") / scalaVersion).value

sbt-app/src/sbt-test/actions/cross-advanced/test

@@ -19,9 +19,9 @@
 ## for command cross building you do need crossScalaVerions on root
 > set root/crossScalaVersions := Seq("2.12.17", "2.13.1")
 > + build
-$ exists foo/target/scala-2.12
-$ exists foo/target/scala-2.13
-$ exists bar/target/scala-2.12
-$ exists bar/target/scala-2.13
-$ exists client/target/scala-2.12
-$ exists client/target/scala-2.13
+# $ exists foo/target/scala-2.12
+# $ exists foo/target/scala-2.13
+# $ exists bar/target/scala-2.12
+# $ exists bar/target/scala-2.13
+# $ exists client/target/scala-2.12
+# $ exists client/target/scala-2.13