Improve ClassLoader layering error message

When a class on the project classpath is loaded via reflection by one of
the parents of the project classloader, sbt run can fail with a
mysterious ClassNotFoundException. This is expected behavior but it
wasn't previously explained to the user.

Ref https://github.com/sbt/sbt/issues/5410.

run/src/main/scala/sbt/Run.scala

@@ -78,7 +78,22 @@ class Run(private[sbt] val newLoader: Seq[File] => ClassLoader, trapExit: Boolea
         val main = getMainMethod(mainClass, loader)
         invokeMain(loader, main, options)
       } catch {
-        case e: java.lang.reflect.InvocationTargetException => throw e.getCause
+        case e: java.lang.reflect.InvocationTargetException =>
+          e.getCause match {
+            case ex: ClassNotFoundException =>
+              val className = ex.getMessage
+              try {
+                loader.loadClass(className)
+                val msg =
+                  s"$className is on the project classpath but not visible to the ClassLoader " +
+                    "that attempted to load it.\n" +
+                    "See https://www.scala-sbt.org/1.x/docs/In-Process-Classloaders.html for " +
+                    "further information."
+                log.error(msg)
+              } catch { case NonFatal(_) => }
+              throw ex
+            case ex => throw ex
+          }
       }
     def directExecute(): Try[Unit] =
       Try(execute()) recover {