[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

libraries/kotlinx-metadata/jvm/build.gradle.kts

@@ -79,7 +79,7 @@ apiValidation {
 }
 
 tasks.dokkaHtml.configure {
-    outputDirectory.set(buildDir.resolve("dokka"))
+    outputDirectory.set(layout.buildDirectory.dir("dokka"))
     pluginsMapConfiguration.set(
         mapOf(
             "org.jetbrains.dokka.base.DokkaBase"