[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/build-tools/src/main/groovy/org/jetbrains/kotlin/NativeInteropPlugin.groovy

@@ -146,15 +146,15 @@ class NamedNativeInteropConfig implements Named {
     }
 
     File getNativeLibsDir() {
-        return new File(project.buildDir, "nativelibs/$target")
+        return project.layout.buildDirectory.dir("nativelibs/$target").get().asFile
     }
 
     File getGeneratedSrcDir() {
-        return new File(project.buildDir, "nativeInteropStubs/$name/kotlin")
+        return project.layout.buildDirectory.dir("nativeInteropStubs/$name/kotlin").get().asFile
     }
 
     File getTemporaryFilesDir() {
-        return new File(project.buildDir, "interopTemp")
+        return project.layout.buildDirectory.dir("interopTemp").get().asFile
     }
 
     String getLlvmDir() {
@@ -213,8 +213,8 @@ class NamedNativeInteropConfig implements Named {
             jvmArgs '-ea'
 
             systemProperties "java.library.path" : project.files(
-                    new File(project.findProject(":kotlin-native:Interop:Indexer").buildDir, "nativelibs"),
-                    new File(project.findProject(":kotlin-native:Interop:Runtime").buildDir, "nativelibs")
+                    project.findProject(":kotlin-native:Interop:Indexer").layout.buildDirectory.dir("nativelibs"),
+                    project.findProject(":kotlin-native:Interop:Runtime").layout.buildDirectory.dir("nativelibs"),
             ).asPath
             // Set the konan.home property because we run the cinterop tool not from a distribution jar
             // so it will not be able to determine this path by itself.

kotlin-native/build-tools/src/main/kotlin/org/jetbrains/kotlin/CopyCommonSources.kt

@@ -16,7 +16,7 @@ open class CopyCommonSources : DefaultTask() {
     val sourcePaths: ConfigurableFileCollection = project.files()
 
     @OutputDirectory
-    var outputDir: File = project.buildDir.resolve("sources")
+    var outputDir: File = project.layout.buildDirectory.get().asFile.resolve("sources")
 
     fun zipSources(needToZip: Boolean) {
         zipSources = needToZip
@@ -46,7 +46,7 @@ open class CopyCommonSources : DefaultTask() {
             val filePrefix = sourcePath.name.replace(Regex("-\\d+.*"), "")
             val targetFileName = "$filePrefix-sources.zip"
 
-            val tempDir = project.buildDir.resolve(name).resolve(filePrefix).also {
+            val tempDir = project.layout.buildDirectory.dir("$name/$filePrefix").get().asFile.also {
                 it.deleteRecursively()
                 it.mkdirs()
             }

kotlin-native/build-tools/src/main/kotlin/org/jetbrains/kotlin/gradle/plugin/konan/KonanPlugin.kt

@@ -89,7 +89,7 @@ internal val Project.konanVersion: String
         ?.toString()
         ?: project.version.toString()
 
-internal val Project.konanBuildRoot          get() = buildDir.resolve("konan")
+internal val Project.konanBuildRoot          get() = layout.buildDirectory.get().asFile.resolve("konan")
 internal val Project.konanBinBaseDir         get() = konanBuildRoot.resolve("bin")
 internal val Project.konanLibsBaseDir        get() = konanBuildRoot.resolve("libs")
 internal val Project.konanBitcodeBaseDir     get() = konanBuildRoot.resolve("bitcode")

kotlin-native/build-tools/src/main/kotlin/org/jetbrains/kotlin/gradle/plugin/konan/tasks/KonanCompileTask.kt

@@ -92,7 +92,7 @@ abstract class KonanCompileTask: KonanBuildingTask(), KonanCompileSpec {
 
     protected fun directoryToKt(dir: Any) = project.fileTree(dir).apply {
         include("**/*.kt")
-        exclude { it.file.startsWith(project.buildDir) }
+        exclude { it.file.startsWith(project.layout.buildDirectory.get().asFile) }
     }
 
     // Command line  ------------------------------------------------------------

kotlin-native/build-tools/src/main/kotlin/org/jetbrains/kotlin/tools/NativePlugin.kt

@@ -121,7 +121,7 @@ open class SourceSet(
         return SourceSet(
             sourceSets,
             name,
-            sourceSets.project.file("${sourceSets.project.buildDir}/$name/${suffixes.first}_${suffixes.second}/"),
+            sourceSets.project.file(sourceSets.project.layout.buildDirectory.dir("$name/${suffixes.first}_${suffixes.second}/")),
             this,
             suffixes
         )
@@ -218,7 +218,7 @@ open class NativeToolsExtension(val project: Project) {
                 dependsOn(it.implicitTasks())
             }
             val deps = objSet.flatMap { it.collection.files }.map { it.path }
-            val toolConfiguration = ToolPatternImpl(sourceSets.extension, "${project.buildDir.path}/$name", *deps.toTypedArray())
+            val toolConfiguration = ToolPatternImpl(sourceSets.extension, "${project.layout.buildDirectory.get().asFile.path}/$name", *deps.toTypedArray())
             toolConfiguration.configuration()
             toolConfiguration.configure(this, false )
         }