[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

wasm/wasm.ir/build.gradle.kts

@@ -26,10 +26,10 @@ repositories {
     }
 }
 
-val wabtDir = File(buildDir, "wabt")
+val wabtDir = File(layout.buildDirectory.get().asFile, "wabt")
 val wabtVersion = "1.0.19"
 val testSuiteRevision = "18f8340"
-val testSuiteDir = File(buildDir, "testsuite")
+val testSuiteDir = File(layout.buildDirectory.get().asFile, "testsuite")
 
 val gradleOs = org.gradle.internal.os.OperatingSystem.current()
 val wabtOS = when {