Fix DENO_V8_FLAGS override and add warning for --js-module-kind + Wasm

- runDeno: append --experimental-wasm-exnref to existing DENO_V8_FLAGS
  instead of silently replacing user-defined flags; log when flag is set
- ScalaJsOptions.linkerConfig: warn when Wasm overrides user-specified
  --js-module-kind (forced to ESModule by Wasm backend)

Author: lostflydev

modules/build/src/main/scala/scala/build/internal/Runner.scala

@@ -367,9 +367,18 @@ object Runner {
         .map(_.toString)
         .toRight(DenoNotFoundError()))
     val denoFlags = Seq("run", "--allow-read")
+    val wasmFlag  = "--experimental-wasm-exnref"
     val extraEnv  =
-      if (emitWasm && denoNeedsWasmFlag) Map("DENO_V8_FLAGS" -> "--experimental-wasm-exnref")
-      else Map.empty
+      if (emitWasm && denoNeedsWasmFlag) {
+        // Append to any existing DENO_V8_FLAGS rather than replacing them.
+        val existing = sys.env.get("DENO_V8_FLAGS").filter(_.nonEmpty)
+        val merged   = existing.fold(wasmFlag)(f => s"$f $wasmFlag")
+        logger.log(
+          s"Wasm: setting DENO_V8_FLAGS=$merged (required for Wasm exception handling)"
+        )
+        Map("DENO_V8_FLAGS" -> merged)
+      }
+      else Map.empty[String, String]
 
     if (allowExecve && Execve.available()) {
       val command = Seq(denoPath) ++ denoFlags ++ Seq(entrypoint.getAbsolutePath) ++ args

modules/options/src/main/scala/scala/build/options/ScalaJsOptions.scala

@@ -155,6 +155,10 @@ final case class ScalaJsOptions(
       esVersion = esVersion(logger)
     )
 
+    if (jsEmitWasm && moduleKindStr.isDefined)
+      logger.message(
+        s"[${Console.YELLOW}warn${Console.RESET}] Wasm mode forces ES module output; --js-module-kind is ignored"
+      )
     ScalaJsLinkerConfig(
       moduleKind =
         if (jsEmitWasm) ScalaJsLinkerConfig.ModuleKind.ESModule else moduleKind(logger),