[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/tools/jdk-api-validator/build.gradle.kts

@@ -25,7 +25,7 @@ dependencies {
     signature("org.codehaus.mojo.signature:java16:1.1@signature")
 }
 
-val signaturesDirectory = buildDir.resolve("signatures")
+val signaturesDirectory = layout.buildDirectory.get().asFile.resolve("signatures")
 
 val collectSignatures by tasks.registering(Sync::class) {
     from(signature)