[Scalafix] Report problems with invalid path and fix flaky behaviour

Two things are done in this PR:
- make sure that if the custom configuration file doesn't exist that we will properly report it to the user
- make sure that Scalafix will always pick up the semanticdb file from the targetroot

The second problem popped up in cases that semanticdb started being written to a different directory (`/target/scala-2.13/meta/`), which meant that Scalafix could pick up the old stale files from .bloop directory.

The change most likely came from sbt, which might have started adding it as the default, but I am not entirely sure why.

metals/src/main/scala/scala/meta/internal/metals/ScalafixProvider.scala

@@ -48,12 +48,8 @@ case class ScalafixProvider(
         val tmp = AbsolutePath(Files.createTempFile("metals", ".scala"))
         tmp.writeText("object Main{}\n")
         for (target <- targets)
-          scalafixEvaluate(
-            tmp,
-            target.scalaVersion,
-            target.scalaBinaryVersion,
-            target.fullClasspath
-          )
+          scalafixEvaluate(tmp, target)
+
         tmp.delete()
       } catch {
         case e: Throwable =>
@@ -79,13 +75,7 @@ case class ScalafixProvider(
       Future.successful(Nil)
     } else {
       compilations.compilationFinished(file).flatMap { _ =>
-        val scalaBinaryVersion = scalaTarget.scalaBinaryVersion
-        val scalafixEvaluation = scalafixEvaluate(
-          file,
-          scalaTarget.scalaVersion,
-          scalaBinaryVersion,
-          scalaTarget.fullClasspath
-        )
+        val scalafixEvaluation = scalafixEvaluate(file, scalaTarget)
 
         scalafixEvaluation match {
           case Failure(exception) =>
@@ -132,18 +122,44 @@ case class ScalafixProvider(
   }
 
   private def scalafixConf: Option[Path] = {
-    val scalafixConfPath = userConfig().scalafixConfigPath
-      .getOrElse(workspace.resolve(".scalafix.conf"))
-    if (scalafixConfPath.isFile) Some(scalafixConfPath.toNIO)
-    else None
+    val defaultLocation = workspace.resolve(".scalafix.conf")
+    userConfig().scalafixConfigPath match {
+      case Some(path) if !path.isFile && defaultLocation.isFile =>
+        languageClient.showMessage(
+          MessageType.Warning,
+          s"No configuration at $path, using default at $defaultLocation."
+        )
+        Some(defaultLocation.toNIO)
+      case Some(path) if !path.isFile =>
+        languageClient.showMessage(
+          MessageType.Warning,
+          s"No configuration at $path, using Scalafix defaults."
+        )
+        None
+      case Some(path) => Some(path.toNIO)
+      case None if defaultLocation.isFile =>
+        Some(defaultLocation.toNIO)
+      case _ => None
+    }
   }
 
   private def scalafixEvaluate(
       file: AbsolutePath,
-      scalaVersion: String,
-      scalaBinaryVersion: String,
-      fullClasspath: java.util.List[Path]
+      scalaTarget: ScalaTarget
   ): Try[ScalafixEvaluation] = {
+    val scalaBinaryVersion = scalaTarget.scalaBinaryVersion
+
+    val targetRoot =
+      buildTargets.scalacOptions(scalaTarget.info.getId()).map {
+        scalacOptions =>
+          scalacOptions.targetroot(scalaTarget.scalaVersion).toNIO
+      }
+    val scalaVersion = scalaTarget.scalaVersion
+    // It seems that Scalafix ignores the targetroot parameter and searches the classpath
+    // Prepend targetroot to make sure that it's picked up first always
+    val classpath =
+      (targetRoot.toList ++ scalaTarget.fullClasspath.asScala).asJava
+
     for {
       api <- getScalafix(scalaBinaryVersion)
       urlClassLoaderWithExternalRule <- getRuleClassLoader(
@@ -158,7 +174,7 @@ case class ScalafixProvider(
       api
         .newArguments()
         .withScalaVersion(scalaVersion)
-        .withClasspath(fullClasspath)
+        .withClasspath(classpath)
         .withToolClasspath(urlClassLoaderWithExternalRule)
         .withConfig(scalafixConf.asJava)
         .withRules(List(organizeImportRuleName).asJava)