[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/Interop/Runtime/build.gradle.kts

@@ -36,7 +36,7 @@ native {
         tool(*hostPlatform.clangForJni.clangCXX("").toTypedArray())
         flags("-shared",
               "-o",ruleOut(), *ruleInAll(),
-              "-L${project(":kotlin-native:libclangext").buildDir}",
+              "-L${project(":kotlin-native:libclangext").layout.buildDirectory.get().asFile}",
               "${nativeDependencies.libffiPath}/lib/libffi.$lib",
               "-lclangext")
     }
@@ -54,7 +54,7 @@ dependencies {
 
 val prepareSharedSourcesForJvm by tasks.registering(Sync::class) {
     from("src/main/kotlin")
-    into("$buildDir/src/main/kotlin")
+    into(project.layout.buildDirectory.dir("src/main/kotlin"))
 }
 val prepareKotlinIdeaImport by tasks.registering {
     dependsOn(prepareSharedSourcesForJvm)
@@ -83,6 +83,6 @@ val nativelibs = project.tasks.create<Copy>("nativelibs") {
     val callbacksSolib = solib("callbacks")
     dependsOn(callbacksSolib)
 
-    from("$buildDir/$callbacksSolib")
-    into("$buildDir/nativelibs/")
+    from(layout.buildDirectory.dir(callbacksSolib))
+    into(layout.buildDirectory.dir("nativelibs"))
 }