Fixed konan.data.dir with caches

Removed TODOs after updating to kotlin bootstrap version with konan.data.dir gradle property changes

Fixed warning of incorrect passing -Xkonan-data-dir arg in konanc from KGP and fixed setting konan-data-dir in SetupConfiguration#setupCommonOptionsForCaches

#KT-60660 Fixed

Merge-request: KT-MR-11299
Merged-by: Dmitrii Krasnov <Dmitrii.Krasnov@jetbrains.com>

kotlin-native/klib/src/main/kotlin/org/jetbrains/kotlin/cli/klib/main.kt

@@ -120,7 +120,6 @@ object KlibToolLogger : Logger, IrMessageLogger {
     }
 }
 
-// TODO(Dmitrii Krasnov): I'm not sure that we should put konan distribution dir here
 val defaultRepository = File(DependencyDirectories.localKonanDir.resolve("klib").absolutePath)
 
 open class ModuleDeserializer(val library: ByteArray) {