[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

prepare/ide-plugin-dependencies/kotlin-backend-native-for-ide/build.gradle.kts

@@ -44,7 +44,7 @@ idePluginDependency {
     val shadowJar by task<ShadowJar> {
         configurations = listOf(embedded)
         duplicatesStrategy = DuplicatesStrategy.FAIL
-        destinationDirectory.set(File(buildDir, "libs"))
+        destinationDirectory.set(layout.buildDirectory.dir("libs"))
         archiveClassifier.set("shadow")
     }
 
@@ -53,7 +53,7 @@ idePluginDependency {
 
         configuration(fileFrom(projectDir, "backend-native-for-ide.pro"))
         injars(mapOf("filter" to "!META-INF/versions/**"), shadowJar.get().outputs.files)
-        outjars(fileFrom(buildDir, "libs", "$jarBaseName-$version-after-proguard.jar"))
+        outjars(layout.buildDirectory.file("libs/$jarBaseName-$version-after-proguard.jar"))
 
         javaLauncher.set(project.getToolchainLauncherFor(JdkMajorVersion.JDK_1_8))