reduce warnings inside flutter.groovy file (#152073)

In the context of [issue #146036](flutter/flutter#146036), the flutter.groovy file, considering [issue #147122](flutter/flutter#147122), currently has only two of the buildDir instances replaced. The other two instances have issues that require more investigation.

Author: AbdeMohlbi

packages/flutter_tools/gradle/src/main/groovy/flutter.groovy

@@ -332,7 +332,7 @@ class FlutterPlugin implements Plugin<Project> {
         // -> Kotlin migration, we should remove this complexity and perform the checks inside
         // of the main Flutter Gradle Plugin.
         // See https://github.com/flutter/flutter/issues/121541#issuecomment-1920363687.
-        final Boolean shouldSkipDependencyChecks = project.hasProperty("skipDependencyChecks") && project.getProperty("skipDependencyChecks");
+        final Boolean shouldSkipDependencyChecks = project.hasProperty("skipDependencyChecks") && project.getProperty("skipDependencyChecks")
         if (!shouldSkipDependencyChecks) {
             try {
                 final String dependencyCheckerPluginPath = Paths.get(flutterRoot.absolutePath,
@@ -1272,7 +1272,7 @@ class FlutterPlugin implements Plugin<Project> {
                 trackWidgetCreation(trackWidgetCreationValue)
                 targetPlatformValues = targetPlatforms
                 sourceDir(getFlutterSourceDirectory())
-                intermediateDir(project.file("${project.buildDir}/$INTERMEDIATES_DIR/flutter/${variant.name}/"))
+                intermediateDir(project.file(project.layout.buildDirectory.dir("$INTERMEDIATES_DIR/flutter/${variant.name}/")))
                 frontendServerStarterPath(frontendServerStarterPathValue)
                 extraFrontEndOptions(extraFrontEndOptionsValue)
                 extraGenSnapshotOptions(extraGenSnapshotOptionsValue)
@@ -1287,7 +1287,7 @@ class FlutterPlugin implements Plugin<Project> {
                 validateDeferredComponents(validateDeferredComponentsValue)
                 flavor(flavorValue)
             }
-            File libJar = project.file("${project.buildDir}/$INTERMEDIATES_DIR/flutter/${variant.name}/libs.jar")
+            File libJar = project.file(project.layout.buildDirectory.dir("$INTERMEDIATES_DIR/flutter/${variant.name}/libs.jar"))
             Task packJniLibsTask = project.tasks.create(name: "packJniLibs${FLUTTER_BUILD_PREFIX}${variant.name.capitalize()}", type: Jar) {
                 destinationDirectory = libJar.parentFile
                 archiveFileName = libJar.name