[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/js-ir-minimal-for-test/build.gradle.kts

@@ -25,7 +25,7 @@ val commonMainFullSources by task<Sync> {
         }
     }
 
-    into("$buildDir/commonMainFullSources")
+    into(layout.buildDirectory.dir("commonMainFullSources"))
 }
 
 val commonMainSources by task<Sync> {
@@ -72,7 +72,7 @@ val commonMainSources by task<Sync> {
         commonMainFullSources.get().outputs.files.singleFile
     }
 
-    into("$buildDir/commonMainSources")
+    into(layout.buildDirectory.dir("commonMainSources"))
 }
 
 val commonMainCollectionSources by task<Sync> {
@@ -82,7 +82,7 @@ val commonMainCollectionSources by task<Sync> {
         commonMainFullSources.get().outputs.files.singleFile
     }
 
-    into("$buildDir/commonMainCollectionSources")
+    into(layout.buildDirectory.dir("commonMainCollectionSources"))
 }
 
 val jsMainSources by task<Sync> {
@@ -131,7 +131,7 @@ val jsMainSources by task<Sync> {
         into("builtins")
     }
 
-    into("$buildDir/jsMainSources")
+    into(layout.buildDirectory.dir("jsMainSources"))
 }
 
 kotlin {