diff --git a/apps/backend/src/publishHandler.ts b/apps/backend/src/publishHandler.ts
index 5b9655157..e8daa692a 100644
--- a/apps/backend/src/publishHandler.ts
+++ b/apps/backend/src/publishHandler.ts
@@ -22,7 +22,7 @@ import {
 import type { UserDataPopulatedRequest } from "@codemod-com/auth";
 import { prisma } from "@codemod-com/database";
 // Direct import because tree-shaking helps this to not throw.
-import { getCodemodExecutable } from "@codemod-com/runner/dist/source-code.js";
+import { BUILT_SOURCE_PATH } from "@codemod-com/runner/dist/source-code.js";
 import {
   buildCodemodSlug,
   codemodNameRegex,
@@ -34,6 +34,7 @@ import {
   unzip,
 } from "@codemod-com/utilities";
 
+import { readFile } from "node:fs/promises";
 import { buildRevalidateHelper } from "./revalidate.js";
 import { environment } from "./util.js";
 
@@ -147,7 +148,10 @@ export const publishHandler: RouteHandler<{
         throwOnNotFound: false,
       });
 
-      const built = await getCodemodExecutable(unpackPath).catch(() => null);
+      const built = await readFile(
+        join(unpackPath, BUILT_SOURCE_PATH),
+        "utf8",
+      ).catch(() => null);
 
       if (path === null || built === null) {
         return reply.code(400).send({
diff --git a/apps/cli/src/commands/init.ts b/apps/cli/src/commands/init.ts
index 5adecd989..7e4f3b078 100644
--- a/apps/cli/src/commands/init.ts
+++ b/apps/cli/src/commands/init.ts
@@ -12,6 +12,11 @@ import inquirer from "inquirer";
 import terminalLink from "terminal-link";
 
 import { type Printer, chalk } from "@codemod-com/printer";
+import {
+  BUILT_SOURCE_PATH,
+  bundleJS,
+  getCodemodExecutable,
+} from "@codemod-com/runner";
 import {
   ALL_ENGINES,
   type KnownEngines,
@@ -31,12 +36,16 @@ import { oraCheckmark } from "#utils/constants.js";
 import { detectCodemodEngine } from "#utils/detectCodemodEngine.js";
 import { isFile } from "#utils/general.js";
 
+// @TODO: decompose
 export const handleInitCliCommand = async (options: {
   printer: Printer;
   target: string;
   source?: string;
   engine?: string;
+  esm?: boolean;
+  build?: boolean;
   noLogs?: boolean;
+  noFixtures?: boolean;
   useDefaultName?: boolean;
 }) => {
   const {
@@ -44,8 +53,11 @@ export const handleInitCliCommand = async (options: {
     target,
     source,
     engine,
-    useDefaultName = false,
+    esm,
+    build = true,
     noLogs = false,
+    noFixtures = false,
+    useDefaultName = false,
   } = options;
 
   if (source) {
@@ -135,6 +147,9 @@ export const handleInitCliCommand = async (options: {
     downloadInput.codemodBody = await readFile(source, "utf-8");
   }
 
+  if (noFixtures) {
+    downloadInput.cases = [];
+  }
   const files = getCodemodProjectFiles(downloadInput);
 
   const codemodBaseDir = join(target ?? process.cwd(), downloadInput.name);
@@ -154,11 +169,7 @@ export const handleInitCliCommand = async (options: {
       });
     } catch (err) {
       for (const createdPath of created) {
-        try {
-          await unlink(join(codemodBaseDir, createdPath));
-        } catch (err) {
-          //
-        }
+        await unlink(join(codemodBaseDir, createdPath)).catch(() => null);
       }
 
       throw new Error(
@@ -172,10 +183,19 @@ export const handleInitCliCommand = async (options: {
     }
   }
 
-  if (noLogs) {
-    return codemodBaseDir;
+  if (build) {
+    const outputPath = join(codemodBaseDir, BUILT_SOURCE_PATH);
+    const bundledCode =
+      source && isSourceAFile
+        ? await bundleJS({ entry: source, output: outputPath, esm })
+        : await getCodemodExecutable(codemodBaseDir, esm);
+
+    await mkdir(dirname(outputPath), { recursive: true });
+    await writeFile(outputPath, bundledCode);
   }
 
+  if (noLogs) return codemodBaseDir;
+
   printer.printConsoleMessage(
     "info",
     chalk.cyan("Codemod package created at", `${chalk.bold(codemodBaseDir)}.`),
diff --git a/apps/cli/src/commands/publish.ts b/apps/cli/src/commands/publish.ts
index b64fb19ec..b684d823c 100644
--- a/apps/cli/src/commands/publish.ts
+++ b/apps/cli/src/commands/publish.ts
@@ -6,6 +6,7 @@ import inquirer from "inquirer";
 import * as semver from "semver";
 import * as v from "valibot";
 
+import { tmpdir } from "node:os";
 import { type Printer, chalk } from "@codemod-com/printer";
 import { BUILT_SOURCE_PATH, getCodemodExecutable } from "@codemod-com/runner";
 import type { TelemetrySender } from "@codemod-com/telemetry";
@@ -23,15 +24,15 @@ import { extractPrintableApiError, getCodemod, publish } from "#api.js";
 import { getCurrentUserOrLogin } from "#auth-utils.js";
 import { handleInitCliCommand } from "#commands/init.js";
 import type { TelemetryEvent } from "#telemetry.js";
-import { codemodDirectoryPath } from "#utils/constants.js";
 import { isFile } from "#utils/general.js";
 
 export const handlePublishCliCommand = async (options: {
   printer: Printer;
   source: string;
   telemetry: TelemetrySender<TelemetryEvent>;
+  esm?: boolean;
 }) => {
-  let { source, printer, telemetry } = options;
+  let { source, printer, telemetry, esm } = options;
 
   const { token, allowedNamespaces, organizations } =
     await getCurrentUserOrLogin({
@@ -39,7 +40,6 @@ export const handlePublishCliCommand = async (options: {
       printer,
     });
 
-  const tempDirectory = join(codemodDirectoryPath, "temp");
   const formData = new FormData();
   const excludedPaths = [
     "node_modules/**",
@@ -53,8 +53,11 @@ export const handlePublishCliCommand = async (options: {
     source = await handleInitCliCommand({
       printer,
       source,
-      target: tempDirectory,
+      target: tmpdir(),
       noLogs: true,
+      noFixtures: true,
+      build: true,
+      esm,
     });
 
     const { choice } = await inquirer.prompt<{ choice: string }>({
@@ -260,7 +263,7 @@ export const handlePublishCliCommand = async (options: {
   );
 
   if (codemodRc.engine !== "recipe") {
-    const builtExecutable = await getCodemodExecutable(source).catch(
+    const builtExecutable = await getCodemodExecutable(source, esm).catch(
       () => null,
     );
 
@@ -315,7 +318,7 @@ export const handlePublishCliCommand = async (options: {
       message: errorMessage,
     });
   } finally {
-    if (source.includes(tempDirectory)) {
+    if (source.includes(tmpdir())) {
       await fs.promises.rm(source, { recursive: true, force: true });
     }
   }
diff --git a/apps/cli/src/fetch-codemod.ts b/apps/cli/src/fetch-codemod.ts
index 716c77782..dcdfd7c52 100644
--- a/apps/cli/src/fetch-codemod.ts
+++ b/apps/cli/src/fetch-codemod.ts
@@ -1,5 +1,6 @@
-import { createHash, randomBytes } from "node:crypto";
-import { lstat, mkdir, writeFile } from "node:fs/promises";
+import { createHash } from "node:crypto";
+import { lstat, mkdir } from "node:fs/promises";
+import { tmpdir } from "node:os";
 import { join, parse as pathParse, resolve } from "node:path";
 import type { AxiosError } from "axios";
 import inquirer from "inquirer";
@@ -7,14 +8,12 @@ import semver from "semver";
 import { flatten } from "valibot";
 
 import { type Printer, chalk } from "@codemod-com/printer";
-import { bundleJS } from "@codemod-com/runner";
 import {
   type Codemod,
   type CodemodValidationInput,
   buildCodemodSlug,
   doubleQuotify,
   getCodemodRc,
-  isJavaScriptName,
   isRecipeCodemod,
   parseCodemod,
   parseEngineOptions,
@@ -123,34 +122,15 @@ export const fetchCodemod = async (options: FetchOptions): Promise<Codemod> => {
       }
 
       // Standalone codemod
-      // For standalone codemods, before creating a compatible package, we attempt to
-      // build the binary because it might have other dependencies in the folder
-      const tempFolderPath = join(codemodDirectoryPath, "temp");
-      await mkdir(tempFolderPath, { recursive: true });
-
-      let codemodPath = nameOrPath;
-      if (isJavaScriptName(nameOrPath)) {
-        codemodPath = join(
-          tempFolderPath,
-          `${randomBytes(8).toString("hex")}.js`,
-        );
-
-        try {
-          const executable = await bundleJS({ entry: nameOrPath });
-          await writeFile(codemodPath, executable);
-        } catch (err) {
-          throw new Error(
-            `Error bundling codemod: ${(err as Error).message ?? "Unknown error"}`,
-          );
-        }
-      }
-
       const codemodPackagePath = await handleInitCliCommand({
         printer,
-        source: codemodPath,
-        target: tempFolderPath,
+        source: nameOrPath,
+        target: tmpdir(),
         useDefaultName: true,
         noLogs: true,
+        noFixtures: true,
+        build: true,
+        esm: argv.esm,
       });
 
       const { config } = await getCodemodRc({
diff --git a/apps/cli/src/flags.ts b/apps/cli/src/flags.ts
index 861e30df4..3727cfe13 100644
--- a/apps/cli/src/flags.ts
+++ b/apps/cli/src/flags.ts
@@ -41,6 +41,12 @@ export const buildGlobalOptions = <T>(y: Argv<T>) =>
       alias: "v",
       description: "Show version number",
     })
+    .option("esm", {
+      type: "boolean",
+      description:
+        "Use to specify that you intend to use ESM-specific features in your codemods.",
+      default: false,
+    })
     .option("json", {
       alias: "j",
       type: "boolean",
diff --git a/apps/cli/src/main.ts b/apps/cli/src/main.ts
index 13474a820..891edfd7b 100644
--- a/apps/cli/src/main.ts
+++ b/apps/cli/src/main.ts
@@ -263,6 +263,7 @@ export const main = async () => {
             printer,
             source: args.source ?? process.cwd(),
             telemetry: telemetryService,
+            esm: args.esm,
           });
         });
       },
@@ -326,6 +327,7 @@ export const main = async () => {
             printer,
             target: args.target ?? process.cwd(),
             engine: args.engine,
+            esm: args.esm,
           }),
         );
       },
diff --git a/apps/cli/src/safe-arguments.ts b/apps/cli/src/safe-arguments.ts
index 52568adc6..fea61da1c 100644
--- a/apps/cli/src/safe-arguments.ts
+++ b/apps/cli/src/safe-arguments.ts
@@ -12,7 +12,11 @@ export const buildSafeArgumentRecord = async (
   if (codemod.type === "standalone") {
     // no checks performed for local codemods
     // b/c no source of truth for the arguments
-    return argvRecord as ArgumentRecord;
+    const { ...safeRecord } = argvRecord;
+    delete safeRecord._;
+    delete safeRecord.include;
+    delete safeRecord.exclude;
+    return safeRecord as ArgumentRecord;
   }
 
   const validateStringArg = (options: {
diff --git a/apps/cli/src/worker.ts b/apps/cli/src/worker.ts
index 84841acce..d13e62560 100644
--- a/apps/cli/src/worker.ts
+++ b/apps/cli/src/worker.ts
@@ -32,7 +32,9 @@ const messageHandler = async (m: unknown) => {
     try {
       message = decodeMainThreadMessage(m);
     } catch (err) {
-      throw new Error(`Failed to decode message: ${String(err)}`);
+      throw new Error(
+        `Failed to decode message: ${String(err)} - ${JSON.stringify(m)}`,
+      );
     }
 
     if (message.kind === "initialization") {
@@ -118,7 +120,6 @@ const messageHandler = async (m: unknown) => {
       kind: "error",
       message: error instanceof Error ? error.message : String(error),
       path: error instanceof PathAwareError ? error.path : undefined,
-      stack: error instanceof Error ? error.stack : undefined,
     } satisfies WorkerThreadMessage);
   }
 };
diff --git a/apps/docs/deploying-codemods/cli.mdx b/apps/docs/deploying-codemods/cli.mdx
index 6b1aa2f20..31b3121fb 100644
--- a/apps/docs/deploying-codemods/cli.mdx
+++ b/apps/docs/deploying-codemods/cli.mdx
@@ -261,6 +261,17 @@ codemod [codemod-name] --format
 
 </ResponseField>
 
+<ResponseField name="--esm" type="boolean">
+  If you want to use ESM-specific features like top-level `await` or `import.meta` in your codemods, you can use this flag.
+
+  <Tip>You can also rename your codemod entry-point file to use `.mjs` or `.mts` extension to omit using this compatibility flag.</Tip>
+
+```bash
+codemod [codemod-name] --json
+```
+
+</ResponseField>
+
 <ResponseField name="--no-cache" type="boolean">
   Can be used to disable caching downloaded codemod files.
 
diff --git a/apps/docs/guides/sharing/publishing-codemods.mdx b/apps/docs/guides/sharing/publishing-codemods.mdx
index 44d89db7c..c314580ac 100644
--- a/apps/docs/guides/sharing/publishing-codemods.mdx
+++ b/apps/docs/guides/sharing/publishing-codemods.mdx
@@ -54,6 +54,8 @@ Creating and publishing a [Codemod-compatible package](/guides/building-codemods
         To generate a [Codemod-compatible package](/guides/building-codemods/package-requirements), Codemod CLI will ask you a few questions about your codemod to generate the [`codemodrc.json` configuration file](/guides/building-codemods/package-requirements#codemodrc-json-reference) automatically for you.
         </Note>
 
+        <Tip>If you want to use ESM-specific features like top-level `await` or `import.meta`, you can rename it to use `.mjs` or `.mts` extension or specify `--esm` flag to treat the source file as ESM package explicitly.</Tip>
+
         ```bash
         codemod publish [path] --source
         ```
diff --git a/apps/frontend/app/(website)/studio/main/RunOptions.tsx b/apps/frontend/app/(website)/studio/main/RunOptions.tsx
index cd43c5fa1..f2fcf1704 100644
--- a/apps/frontend/app/(website)/studio/main/RunOptions.tsx
+++ b/apps/frontend/app/(website)/studio/main/RunOptions.tsx
@@ -41,6 +41,19 @@ export const RunOptions = () => {
   const modStore = useModStore();
   const { engine, getAllSnippets } = useSnippetsStore();
 
+  const allSnippets = getAllSnippets();
+  const cases = allSnippets.before.reduce(
+    (acc, before, i) => {
+      const after = allSnippets.after[i];
+      if (!after) {
+        return acc;
+      }
+
+      return acc.concat({ before, after });
+    },
+    [] as { before: string; after: string }[],
+  );
+
   const { session } = useSession();
   const { getToken } = useAuth();
 
@@ -77,17 +90,7 @@ export const RunOptions = () => {
       // TODO: temporary fix, most likely we need to upgrade monaco editor or babel or whatever is responsible
       // for taking the code from the web-editor and converting it to string
       codemodBody: modStore.content.replace(/\n *as\n *const/g, " as const"),
-      cases: allSnippets.before.reduce(
-        (acc, before, i) => {
-          const after = allSnippets.after[i];
-          if (!after) {
-            return acc;
-          }
-
-          return acc.concat({ before, after });
-        },
-        [] as { before: string; after: string }[],
-      ),
+      cases: cases.length ? cases : undefined,
       engine,
       username: session.user.username ?? session.user.fullName,
     });
diff --git a/packages/printer/src/schemata/worker-thread.ts b/packages/printer/src/schemata/worker-thread.ts
index f4c8e5b93..89e4b3917 100644
--- a/packages/printer/src/schemata/worker-thread.ts
+++ b/packages/printer/src/schemata/worker-thread.ts
@@ -12,7 +12,6 @@ const workerThreadMessageSchema = v.union([
     kind: v.literal("error"),
     message: v.string(),
     path: v.optional(v.string()),
-    stack: v.optional(v.string()),
   }),
   v.object({
     kind: v.literal("console"),
diff --git a/packages/runner/src/runner.ts b/packages/runner/src/runner.ts
index f3e8bb6c8..b755daf8d 100644
--- a/packages/runner/src/runner.ts
+++ b/packages/runner/src/runner.ts
@@ -122,7 +122,7 @@ export class Runner {
   }) {
     const { codemod, flowSettings, onError, onSuccess, printer } = options;
     const cloudRunner = await this._options.runnerService?.startCodemodRun({
-      source: await getCodemodExecutable(codemod.path),
+      source: await getCodemodExecutable(codemod.path, flowSettings.esm),
       engine: codemod.config.engine as "workflow",
       args: codemod.safeArgumentRecord,
     });
@@ -484,7 +484,10 @@ export class Runner {
       return await onSuccess?.({ codemod, output: "", commands: [] });
     }
 
-    const codemodSource = await getCodemodExecutable(codemod.path);
+    const codemodSource = await getCodemodExecutable(
+      codemod.path,
+      flowSettings.esm,
+    );
     const transformer = await getTransformer(codemodSource);
 
     if (codemod.config.engine === "workflow") {
diff --git a/packages/runner/src/schemata/flow-settings.ts b/packages/runner/src/schemata/flow-settings.ts
index f31005c95..2bb16c2bd 100644
--- a/packages/runner/src/schemata/flow-settings.ts
+++ b/packages/runner/src/schemata/flow-settings.ts
@@ -46,6 +46,7 @@ export const flowSettingsSchema = v.object({
   json: v.optional(v.boolean(), DEFAULT_USE_JSON),
   threads: v.optional(v.pipe(v.number(), v.minValue(0)), DEFAULT_THREAD_COUNT),
   cloud: v.optional(v.boolean(), false),
+  esm: v.optional(v.boolean(), false),
 });
 
 export type FlowSettings = v.InferOutput<typeof flowSettingsSchema>;
diff --git a/packages/runner/src/source-code.ts b/packages/runner/src/source-code.ts
index 09ec61d9e..8408480cd 100644
--- a/packages/runner/src/source-code.ts
+++ b/packages/runner/src/source-code.ts
@@ -1,5 +1,5 @@
 import { createHash } from "node:crypto";
-import { mkdir, readFile, writeFile } from "node:fs/promises";
+import { readFile, writeFile } from "node:fs/promises";
 import { dirname, join, resolve } from "node:path";
 import esbuild from "esbuild";
 
@@ -11,7 +11,7 @@ export type TransformFunction = (
 ) => unknown | Promise<unknown>;
 
 type NonDefaultExports = {
-  __esModule?: true;
+  __esModule?: boolean;
   default?: TransformFunction;
   handleSourceFile?: TransformFunction;
   transform?: TransformFunction;
@@ -20,6 +20,9 @@ type NonDefaultExports = {
   filemod?: TransformFunction;
 };
 
+export const isESMExtension = (path: string) =>
+  path.endsWith(".mjs") || path.endsWith(".mts");
+
 export const temporaryLoadedModules = new Map<
   string,
   TransformFunction | null
@@ -52,12 +55,11 @@ export const getTransformer = async (source: string, name?: string) => {
   } catch (err) {
     // ESM
     try {
-      const tempDir = tmpdir();
-      const tempFilePath = join(tempDir, `temp-module-${hashDigest}.mjs`);
-
-      const alreadyLoaded = temporaryLoadedModules.get(tempFilePath);
+      const alreadyLoaded = temporaryLoadedModules.get(hashDigest);
       if (alreadyLoaded) return alreadyLoaded;
 
+      const tempFilePath = join(tmpdir(), `temp-module-${hashDigest}.mjs`);
+
       await writeFile(tempFilePath, source);
       const module = (await import(
         `file://${tempFilePath}`
@@ -76,10 +78,9 @@ export const getTransformer = async (source: string, name?: string) => {
               null
             : null;
 
-      temporaryLoadedModules.set(tempFilePath, transformer);
+      temporaryLoadedModules.set(hashDigest, transformer);
       return transformer;
     } catch (err) {
-      console.log(err);
       return null;
     }
   }
@@ -95,24 +96,25 @@ export const bundleJS = async (options: {
   const {
     entry,
     output = join(dirname(entry), BUILT_SOURCE_PATH),
-    esm = true,
+    esm: argvEsm,
   } = options;
+  const isESM = isESMExtension(entry) || argvEsm;
   const EXTERNAL_DEPENDENCIES = ["jscodeshift", "ts-morph", "@ast-grep/napi"];
 
   const buildOptions: Parameters<typeof esbuild.build>[0] = {
     entryPoints: [entry],
     bundle: true,
-    external: esm ? undefined : EXTERNAL_DEPENDENCIES,
+    external: isESM ? undefined : EXTERNAL_DEPENDENCIES,
     platform: "node",
     minify: true,
     minifyWhitespace: true,
-    format: esm ? "esm" : "cjs",
+    format: isESM ? "esm" : "cjs",
     legalComments: "inline",
     outfile: output,
     write: false, // to the in-memory file system
     logLevel: "error",
-    mainFields: esm ? ["module", "main"] : undefined,
-    banner: esm
+    mainFields: isESM ? ["module", "main"] : undefined,
+    banner: isESM
       ? {
           js: `
 import { fileURLToPath } from 'url';
@@ -141,7 +143,7 @@ const require = createRequire(import.meta.url);
   return sourceCode;
 };
 
-export const getCodemodExecutable = async (source: string, write?: boolean) => {
+export const getCodemodExecutable = async (source: string, esm?: boolean) => {
   const outputFilePath = join(resolve(source), BUILT_SOURCE_PATH);
   try {
     return await readFile(outputFilePath, { encoding: "utf8" });
@@ -158,15 +160,5 @@ export const getCodemodExecutable = async (source: string, write?: boolean) => {
     return readFile(entryPoint, { encoding: "utf8" });
   }
 
-  const bundledCode = await bundleJS({
-    entry: entryPoint,
-    output: outputFilePath,
-  });
-
-  if (write) {
-    await mkdir(dirname(outputFilePath), { recursive: true });
-    await writeFile(outputFilePath, bundledCode);
-  }
-
-  return bundledCode;
+  return bundleJS({ entry: entryPoint, output: outputFilePath, esm });
 };
diff --git a/packages/utilities/src/package-boilerplate.ts b/packages/utilities/src/package-boilerplate.ts
index fe5dfa9c6..83f67b8be 100644
--- a/packages/utilities/src/package-boilerplate.ts
+++ b/packages/utilities/src/package-boilerplate.ts
@@ -668,7 +668,7 @@ export function getCodemodProjectFiles(input: ProjectDownloadInput) {
       throw new Error(`Unknown engine: ${input.engine}`);
   }
 
-  if (!input.cases || input.cases.length === 0) {
+  if (input.cases === undefined) {
     input.cases = [
       {
         before: `const toReplace = "hello";`,