Fix classpath filter in run

We were incorrectly building the dependency layer in the run task using
the raw jars from dependencyClasspath rather than the actual classpath
jars (which may be different if bgCopyClasspath is true -- which it is
by default). This was preventing spark from working with AllLibraryJars
because it would load its classes and resources from the coursier cache
but the classpath filter would reject the resources because they came
from the coursier cache instead of the classpath.

main/src/main/scala/sbt/internal/ClassLoaders.scala

@@ -79,12 +79,14 @@ private[sbt] object ClassLoaders {
         val allDeps = dependencyJars(dependencyClasspath).value.filterNot(exclude)
         val newLoader =
           (classpath: Seq[File]) => {
+            val mappings = classpath.map(f => f.getName -> f).toMap
+            val transformedDependencies = allDeps.map(f => mappings.get(f.getName).getOrElse(f))
             buildLayers(
               strategy = classLoaderLayeringStrategy.value: @sbtUnchecked,
               si = instance,
               fullCP = classpath.map(f => f -> IO.getModifiedTimeOrZero(f)),
               resourceCP = resourceCP,
-              allDependencies = allDeps,
+              allDependencies = transformedDependencies,
               cache = extendedClassLoaderCache.value: @sbtUnchecked,
               resources = ClasspathUtilities.createClasspathResources(classpath, instance),
               tmp = taskTemporaryDirectory.value: @sbtUnchecked,