[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/Indexer/build.gradle.kts

@@ -22,7 +22,7 @@ plugins {
 
 val libclangextProject = project(":kotlin-native:libclangext")
 val libclangextTask = libclangextProject.path + ":build"
-val libclangextDir = libclangextProject.buildDir
+val libclangextDir = libclangextProject.layout.buildDirectory.get().asFile
 val libclangextIsEnabled = libclangextProject.findProperty("isEnabled")!! as Boolean
 
 
@@ -148,8 +148,8 @@ val nativelibs = project.tasks.register<Copy>("nativelibs") {
     val clangstubsSolib = solib("clangstubs")
     dependsOn(clangstubsSolib)
 
-    from("$buildDir/$clangstubsSolib")
-    into("$buildDir/nativelibs/")
+    from(layout.buildDirectory.dir(clangstubsSolib))
+    into(layout.buildDirectory.dir("nativelibs"))
 }
 
 kotlinNativeInterop {
@@ -183,7 +183,7 @@ tasks.withType<Test>().configureEach {
     dependsOn(projectsWithNativeLibs.map { "${it.path}:nativelibs" })
     dependsOn(nativeDependencies.llvmDependency)
     systemProperty("java.library.path", projectsWithNativeLibs.joinToString(File.pathSeparator) {
-        File(it.buildDir, "nativelibs").absolutePath
+        it.layout.buildDirectory.dir("nativelibs").get().asFile.absolutePath
     })
 
     systemProperty("kotlin.native.llvm.libclang", "${nativeDependencies.llvmPath}/" + if (HostManager.hostIsMingw) {
@@ -192,7 +192,7 @@ tasks.withType<Test>().configureEach {
         "lib/${System.mapLibraryName("clang")}"
     })
 
-    systemProperty("kotlin.native.interop.indexer.temp", File(buildDir, "testTemp"))
+    systemProperty("kotlin.native.interop.indexer.temp", layout.buildDirectory.dir("testTemp").get().asFile)
 }
 
 // Please note that list of headers should be fixed manually.
@@ -202,14 +202,14 @@ tasks.register("updatePrebuilt") {
 
     doLast {
         copy {
-            from("$buildDir/nativeInteropStubs/clang/kotlin") {
+            from(layout.buildDirectory.dir("nativeInteropStubs/clang/kotlin")) {
                 include("clang/clang.kt")
             }
             into("prebuilt/nativeInteropStubs/kotlin")
         }
 
         copy {
-            from("$buildDir/interopTemp") {
+            from(layout.buildDirectory.dir("interopTemp")) {
                 include("clangstubs.c")
             }
             into("prebuilt/nativeInteropStubs/c")