[Build] Migrate most of the build logic from Project.buildDir usage

It's going to be deprecated in Gradle 8.3

There's currently no way to pass a `org.gradle.api.provider.Provider` to the JavaExec.systemProperty or Test.systemProperty. There's a workaround using `org.gradle.process.CommandLineArgumentProvider`, but I intentionally don't rework these calls as Gradle is going to allow passing providers to configure system properties: https://github.com/gradle/gradle/issues/12247#issuecomment-1568427242
^KTI-1473 In Progress

kotlin-native/common/build.gradle.kts

@@ -33,5 +33,5 @@ tasks.register("build") {
 }
 
 tasks.register<Delete>("clean") {
-    delete(buildDir)
+    delete(layout.buildDirectory)
 }