fix(npm): support cjs entrypoint in node_modules folder (#21224)

Closes #21109

cli/tests/integration/npm_tests.rs

@@ -2653,3 +2653,24 @@ pub fn different_nested_dep_byonm() {
     .run();
   output.assert_matches_file("npm/different_nested_dep/main.out");
 }
+
+#[test]
+pub fn run_cjs_in_node_modules_folder() {
+  let test_context = TestContextBuilder::for_npm().use_temp_cwd().build();
+  let temp_dir = test_context.temp_dir();
+  temp_dir.write("package.json", "{}");
+  temp_dir.write("deno.json", r#"{ "unstable": ["byonm"] }"#);
+  let pkg_dir = temp_dir.path().join("node_modules/package");
+  pkg_dir.create_dir_all();
+  pkg_dir
+    .join("package.json")
+    .write(r#"{ "name": "package" }"#);
+  pkg_dir
+    .join("main.js")
+    .write("console.log('hi'); module.exports = 'hi';");
+  test_context
+    .new_command()
+    .args("run node_modules/package/main.js")
+    .run()
+    .assert_matches_text("hi\n");
+}

cli/tools/run/mod.rs

@@ -45,8 +45,8 @@ To grant permissions, set them before the script argument. For example:
   let http_client = factory.http_client();
   let cli_options = factory.cli_options();
 
-  // Run a background task that checks for available upgrades. If an earlier
-  // run of this background task found a new version of Deno.
+  // Run a background task that checks for available upgrades or output
+  // if an earlier run of this background task found a new version of Deno.
   super::upgrade::check_for_upgrades(
     http_client.clone(),
     deno_dir.upgrade_check_file_path(),

cli/worker.rs

@@ -495,7 +495,9 @@ impl CliMainWorkerFactory {
       }
 
       (node_resolution.into_url(), is_main_cjs)
-    } else if shared.options.is_npm_main {
+    } else if shared.options.is_npm_main
+      || shared.node_resolver.in_npm_package(&main_module)
+    {
       let node_resolution =
         shared.node_resolver.url_to_node_resolution(main_module)?;
       let is_main_cjs = matches!(node_resolution, NodeResolution::CommonJs(_));