[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

plugins/atomicfu/atomicfu-compiler/build.gradle.kts

@@ -168,7 +168,7 @@ projectTest(jUnitMode = JUnitMode.JUnit5) {
         // Exclude all tests with the "atomicfu-native" tag. They should be launched by another test task.
         excludeTags("atomicfu-native")
     }
-    useJsIrBoxTests(version = version, buildDir = "$buildDir/")
+    useJsIrBoxTests(version = version, buildDir = layout.buildDirectory)
 
     workingDir = rootDir