[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/stdlib/build.gradle.kts

@@ -46,10 +46,10 @@ dependencies {
 }
 
 val builtinsDir = "${rootDir}/core/builtins"
-val builtinsSrcDir = "${buildDir}/src/builtin-sources"
+val builtinsSrcDir = "${layout.buildDirectory.get().asFile}/src/builtin-sources"
 
 val jsDir = "${projectDir}/js"
-val jsBuiltinsSrcDir = "${buildDir}/src/js-builtin-sources"
+val jsBuiltinsSrcDir = "${layout.buildDirectory.get().asFile}/src/js-builtin-sources"
 
 val commonOptIns = listOf(
     "kotlin.ExperimentalMultiplatform",
@@ -473,7 +473,7 @@ kotlin {
                     }
                 }
 
-                into("$buildDir/src/wasm-builtin-sources")
+                into(layout.buildDirectory.dir("src/wasm-builtin-sources"))
             }
 
         }
@@ -527,7 +527,7 @@ kotlin {
                 val prepareKotlinTestCommonNativeSources by tasks.registering(Sync::class) {
                     from("../kotlin.test/common/src/main/kotlin")
                     from("../kotlin.test/annotations-common/src/main/kotlin")
-                    into("$buildDir/src/native-kotlin-test-common-sources")
+                    into(layout.buildDirectory.dir("src/native-kotlin-test-common-sources"))
                 }
 
                 kotlin {
@@ -642,13 +642,13 @@ tasks {
         from(jsJar)
         rename { _ -> "full-runtime.klib" }
         // some tests expect stdlib-js klib in this location
-        into(rootProject.buildDir.resolve("js-ir-runtime"))
+        into(rootProject.layout.buildDirectory.dir("js-ir-runtime"))
     }
 
     val jsRearrangedSourcesJar by registering(Jar::class) {
         archiveClassifier.set("js-sources")
         archiveVersion.set("")
-        destinationDirectory.set(file("$buildDir/lib"))
+        destinationDirectory.set(layout.buildDirectory.dir("lib"))
 
         includeEmptyDirs = false
         duplicatesStrategy = DuplicatesStrategy.FAIL