feat: default to TS for file extension and support ext flag in more scenarios (#25472)

Closes #11220
Currently does lint, fmt, and repl

38 files changed, 257 insertions, 69 deletions

diff --git a/.dprint.json b/.dprint.json
index 0acfb5ca3..6ee3db3c5 100644
--- a/.dprint.json
+++ b/.dprint.json
@@ -39,10 +39,14 @@
     "tests/node_compat/runner/TODO.md",
     "tests/node_compat/test",
     "tests/registry/",
+    "tests/specs/bench/default_ts",
     "tests/specs/fmt",
     "tests/specs/lint/bom",
+    "tests/specs/lint/default_ts",
     "tests/specs/lint/syntax_error_reporting",
     "tests/specs/publish/no_check_surfaces_syntax_error",
+    "tests/specs/run/default_ts",
+    "tests/specs/test/default_ts",
     "tests/testdata/byte_order_mark.ts",
     "tests/testdata/encoding",
     "tests/testdata/file_extensions/ts_with_js_extension.js",
diff --git a/cli/args/flags.rs b/cli/args/flags.rs
index 5d3929748..d66ee253f 100644
--- a/cli/args/flags.rs
+++ b/cli/args/flags.rs
@@ -299,7 +299,6 @@ pub struct LintFlags {
   pub json: bool,
   pub compact: bool,
   pub watch: Option<WatchFlags>,
-  pub ext: Option<String>,
 }
 
 impl LintFlags {
@@ -1629,6 +1628,7 @@ If you specify a directory instead of a file, the path is expanded to all contai
       .arg(no_clear_screen_arg())
       .arg(script_arg().last(true))
       .arg(env_file_arg())
+      .arg(executable_ext_arg())
   })
 }
 
@@ -2125,9 +2125,6 @@ Ignore formatting a file by adding an ignore comment at the top of the file:
         Arg::new("ext")
           .long("ext")
           .help("Set content type of the supplied file")
-          // prefer using ts for formatting instead of js because ts works in more scenarios
-          .default_value("ts")
-          .hide_default_value(true)
           .value_parser([
             "ts", "tsx", "js", "jsx", "md", "json", "jsonc", "css", "scss",
             "sass", "less", "html", "svelte", "vue", "astro", "yml", "yaml",
@@ -2910,6 +2907,7 @@ or <c>**/__tests__/**</>:
           .action(ArgAction::SetTrue)
       )
       .arg(env_file_arg())
+      .arg(executable_ext_arg())
     )
 }
 
@@ -4074,6 +4072,7 @@ fn bench_parse(
   flags.type_check_mode = TypeCheckMode::Local;
 
   runtime_args_parse(flags, matches, true, false)?;
+  ext_arg_parse(flags, matches);
 
   // NOTE: `deno bench` always uses `--no-prompt`, tests shouldn't ever do
   // interactive prompts, unless done by user code
@@ -4597,8 +4596,9 @@ fn lint_parse(
   matches: &mut ArgMatches,
 ) -> clap::error::Result<()> {
   unstable_args_parse(flags, matches, UnstableArgsConfig::ResolutionOnly);
-
+  ext_arg_parse(flags, matches);
   config_args_parse(flags, matches);
+
   let files = match matches.remove_many::<String>("files") {
     Some(f) => f.collect(),
     None => vec![],
@@ -4625,7 +4625,6 @@ fn lint_parse(
 
   let json = matches.get_flag("json");
   let compact = matches.get_flag("compact");
-  let ext = matches.remove_one::<String>("ext");
 
   flags.subcommand = DenoSubcommand::Lint(LintFlags {
     files: FileFlags {
@@ -4640,7 +4639,6 @@ fn lint_parse(
     json,
     compact,
     watch: watch_arg_parse(matches)?,
-    ext,
   });
   Ok(())
 }
@@ -4821,6 +4819,8 @@ fn test_parse(
 ) -> clap::error::Result<()> {
   flags.type_check_mode = TypeCheckMode::Local;
   runtime_args_parse(flags, matches, true, true)?;
+  ext_arg_parse(flags, matches);
+
   // NOTE: `deno test` always uses `--no-prompt`, tests shouldn't ever do
   // interactive prompts, unless done by user code
   flags.permissions.no_prompt = true;
@@ -6273,7 +6273,6 @@ mod tests {
           unstable_yaml: false,
           watch: Default::default(),
         }),
-        ext: Some("ts".to_string()),
         ..Flags::default()
       }
     );
@@ -6300,7 +6299,6 @@ mod tests {
           unstable_yaml: false,
           watch: Default::default(),
         }),
-        ext: Some("ts".to_string()),
         ..Flags::default()
       }
     );
@@ -6327,7 +6325,6 @@ mod tests {
           unstable_yaml: false,
           watch: Default::default(),
         }),
-        ext: Some("ts".to_string()),
         ..Flags::default()
       }
     );
@@ -6354,7 +6351,6 @@ mod tests {
           unstable_yaml: false,
           watch: Some(Default::default()),
         }),
-        ext: Some("ts".to_string()),
         ..Flags::default()
       }
     );
@@ -6394,7 +6390,6 @@ mod tests {
             exclude: vec![],
           })
         }),
-        ext: Some("ts".to_string()),
         ..Flags::default()
       }
     );
@@ -6428,7 +6423,6 @@ mod tests {
           unstable_yaml: false,
           watch: Some(Default::default()),
         }),
-        ext: Some("ts".to_string()),
         ..Flags::default()
       }
     );
@@ -6455,7 +6449,6 @@ mod tests {
           unstable_yaml: false,
           watch: Default::default(),
         }),
-        ext: Some("ts".to_string()),
         config_flag: ConfigFlag::Path("deno.jsonc".to_string()),
         ..Flags::default()
       }
@@ -6491,7 +6484,6 @@ mod tests {
           watch: Some(Default::default()),
         }),
         config_flag: ConfigFlag::Path("deno.jsonc".to_string()),
-        ext: Some("ts".to_string()),
         ..Flags::default()
       }
     );
@@ -6530,7 +6522,6 @@ mod tests {
           unstable_yaml: false,
           watch: Default::default(),
         }),
-        ext: Some("ts".to_string()),
         ..Flags::default()
       }
     );
@@ -6564,7 +6555,6 @@ mod tests {
           unstable_yaml: false,
           watch: Default::default(),
         }),
-        ext: Some("ts".to_string()),
         ..Flags::default()
       }
     );
@@ -6589,7 +6579,6 @@ mod tests {
           json: false,
           compact: false,
           watch: Default::default(),
-          ext: None,
         }),
         ..Flags::default()
       }
@@ -6618,7 +6607,6 @@ mod tests {
           json: false,
           compact: false,
           watch: Some(Default::default()),
-          ext: None,
         }),
         ..Flags::default()
       }
@@ -6652,7 +6640,6 @@ mod tests {
             no_clear_screen: true,
             exclude: vec![],
           }),
-          ext: None,
         }),
         ..Flags::default()
       }
@@ -6680,7 +6667,6 @@ mod tests {
           json: false,
           compact: false,
           watch: Default::default(),
-          ext: None,
         }),
         ..Flags::default()
       }
@@ -6703,7 +6689,6 @@ mod tests {
           json: false,
           compact: false,
           watch: Default::default(),
-          ext: None,
         }),
         ..Flags::default()
       }
@@ -6731,7 +6716,6 @@ mod tests {
           json: false,
           compact: false,
           watch: Default::default(),
-          ext: None,
         }),
         ..Flags::default()
       }
@@ -6760,7 +6744,6 @@ mod tests {
           json: false,
           compact: false,
           watch: Default::default(),
-          ext: None,
         }),
         ..Flags::default()
       }
@@ -6783,7 +6766,6 @@ mod tests {
           json: true,
           compact: false,
           watch: Default::default(),
-          ext: None,
         }),
         ..Flags::default()
       }
@@ -6813,7 +6795,6 @@ mod tests {
           json: true,
           compact: false,
           watch: Default::default(),
-          ext: None,
         }),
         config_flag: ConfigFlag::Path("Deno.jsonc".to_string()),
         ..Flags::default()
@@ -6844,7 +6825,6 @@ mod tests {
           json: false,
           compact: true,
           watch: Default::default(),
-          ext: None,
         }),
         config_flag: ConfigFlag::Path("Deno.jsonc".to_string()),
         ..Flags::default()
diff --git a/cli/args/mod.rs b/cli/args/mod.rs
index 0851dfd6c..c4dda95ce 100644
--- a/cli/args/mod.rs
+++ b/cli/args/mod.rs
@@ -1131,7 +1131,7 @@ impl CliOptions {
         resolve_url_or_path(&compile_flags.source_file, self.initial_cwd())?
       }
       DenoSubcommand::Eval(_) => {
-        resolve_url_or_path("./$deno$eval", self.initial_cwd())?
+        resolve_url_or_path("./$deno$eval.ts", self.initial_cwd())?
       }
       DenoSubcommand::Repl(_) => {
         resolve_url_or_path("./$deno$repl.ts", self.initial_cwd())?
diff --git a/cli/cache/mod.rs b/cli/cache/mod.rs
index 86b65bc53..a95c35086 100644
--- a/cli/cache/mod.rs
+++ b/cli/cache/mod.rs
@@ -108,7 +108,7 @@ pub use deno_cache_dir::HttpCache;
 /// a concise interface to the DENO_DIR when building module graphs.
 pub struct FetchCacher {
   file_fetcher: Arc<FileFetcher>,
-  file_header_overrides: HashMap<ModuleSpecifier, HashMap<String, String>>,
+  pub file_header_overrides: HashMap<ModuleSpecifier, HashMap<String, String>>,
   global_http_cache: Arc<GlobalHttpCache>,
   npm_resolver: Arc<dyn CliNpmResolver>,
   module_info_cache: Arc<ModuleInfoCache>,
diff --git a/cli/file_fetcher.rs b/cli/file_fetcher.rs
index ca8fcbee4..2f4b0b3dc 100644
--- a/cli/file_fetcher.rs
+++ b/cli/file_fetcher.rs
@@ -138,11 +138,20 @@ fn fetch_local(specifier: &ModuleSpecifier) -> Result<File, AnyError> {
   let local = specifier.to_file_path().map_err(|_| {
     uri_error(format!("Invalid file path.\n  Specifier: {specifier}"))
   })?;
+  // If it doesnt have a extension, we want to treat it as typescript by default
+  let headers = if local.extension().is_none() {
+    Some(HashMap::from([(
+      "content-type".to_string(),
+      "application/typescript".to_string(),
+    )]))
+  } else {
+    None
+  };
   let bytes = fs::read(local)?;
 
   Ok(File {
     specifier: specifier.clone(),
-    maybe_headers: None,
+    maybe_headers: headers,
     source: bytes.into(),
   })
 }
diff --git a/cli/graph_container.rs b/cli/graph_container.rs
index 9f049946f..211b278e0 100644
--- a/cli/graph_container.rs
+++ b/cli/graph_container.rs
@@ -65,6 +65,7 @@ impl MainModuleGraphContainer {
   pub async fn check_specifiers(
     &self,
     specifiers: &[ModuleSpecifier],
+    ext_overwrite: Option<&String>,
   ) -> Result<(), AnyError> {
     let mut graph_permit = self.acquire_update_permit().await;
     let graph = graph_permit.graph_mut();
@@ -76,6 +77,7 @@ impl MainModuleGraphContainer {
         false,
         self.cli_options.ts_type_lib_window(),
         FetchPermissionsOption::AllowAll,
+        ext_overwrite,
       )
       .await?;
     graph_permit.commit();
@@ -94,7 +96,7 @@ impl MainModuleGraphContainer {
       log::warn!("{} No matching files found.", colors::yellow("Warning"));
     }
 
-    self.check_specifiers(&specifiers).await
+    self.check_specifiers(&specifiers, None).await
   }
 
   pub fn collect_specifiers(
diff --git a/cli/lsp/language_server.rs b/cli/lsp/language_server.rs
index 5f6e38082..6626767dd 100644
--- a/cli/lsp/language_server.rs
+++ b/cli/lsp/language_server.rs
@@ -1420,6 +1420,7 @@ impl Inner {
               document.content(),
               &fmt_options,
               &unstable_options,
+              None,
             )
           }
         };
diff --git a/cli/lsp/testing/execution.rs b/cli/lsp/testing/execution.rs
index 55d81f342..88fb496e4 100644
--- a/cli/lsp/testing/execution.rs
+++ b/cli/lsp/testing/execution.rs
@@ -235,7 +235,7 @@ impl TestRun {
     )?;
     let main_graph_container = factory.main_module_graph_container().await?;
     main_graph_container
-      .check_specifiers(&self.queue.iter().cloned().collect::<Vec<_>>())
+      .check_specifiers(&self.queue.iter().cloned().collect::<Vec<_>>(), None)
       .await?;
 
     let (concurrent_jobs, fail_fast) =
diff --git a/cli/module_loader.rs b/cli/module_loader.rs
index 86824cd70..a81c5a0aa 100644
--- a/cli/module_loader.rs
+++ b/cli/module_loader.rs
@@ -105,11 +105,32 @@ impl ModuleLoadPreparer {
     is_dynamic: bool,
     lib: TsTypeLib,
     permissions: crate::file_fetcher::FetchPermissionsOption,
+    ext_overwrite: Option<&String>,
   ) -> Result<(), AnyError> {
     log::debug!("Preparing module load.");
     let _pb_clear_guard = self.progress_bar.clear_guard();
 
     let mut cache = self.module_graph_builder.create_fetch_cacher(permissions);
+    if let Some(ext) = ext_overwrite {
+      let maybe_content_type = match ext.as_str() {
+        "ts" => Some("text/typescript"),
+        "tsx" => Some("text/tsx"),
+        "js" => Some("text/javascript"),
+        "jsx" => Some("text/jsx"),
+        _ => None,
+      };
+      if let Some(content_type) = maybe_content_type {
+        for root in roots {
+          cache.file_header_overrides.insert(
+            root.clone(),
+            std::collections::HashMap::from([(
+              "content-type".to_string(),
+              content_type.to_string(),
+            )]),
+          );
+        }
+      }
+    }
     log::debug!("Building module graph.");
     let has_type_checked = !graph.roots.is_empty();
 
@@ -763,6 +784,7 @@ impl<TGraphContainer: ModuleGraphContainer> ModuleLoader
           is_dynamic,
           lib,
           root_permissions.into(),
+          None,
         )
         .await?;
       update_permit.commit();
diff --git a/cli/tools/bench/mod.rs b/cli/tools/bench/mod.rs
index f133759c9..be5d0ad0e 100644
--- a/cli/tools/bench/mod.rs
+++ b/cli/tools/bench/mod.rs
@@ -442,7 +442,9 @@ pub async fn run_benchmarks(
   }
 
   let main_graph_container = factory.main_module_graph_container().await?;
-  main_graph_container.check_specifiers(&specifiers).await?;
+  main_graph_container
+    .check_specifiers(&specifiers, cli_options.ext_flag().as_ref())
+    .await?;
 
   if workspace_bench_options.no_run {
     return Ok(());
@@ -569,7 +571,7 @@ pub async fn run_benchmarks_with_watch(
         factory
           .main_module_graph_container()
           .await?
-          .check_specifiers(&specifiers)
+          .check_specifiers(&specifiers, cli_options.ext_flag().as_ref())
           .await?;
 
         if workspace_bench_options.no_run {
diff --git a/cli/tools/check.rs b/cli/tools/check.rs
index 9c464fa16..c22afbb9a 100644
--- a/cli/tools/check.rs
+++ b/cli/tools/check.rs
@@ -73,7 +73,7 @@ pub async fn check(
   };
 
   main_graph_container
-    .check_specifiers(&specifiers_for_typecheck)
+    .check_specifiers(&specifiers_for_typecheck, None)
     .await
 }
 
diff --git a/cli/tools/fmt.rs b/cli/tools/fmt.rs
index 17ddf6c65..3f927545d 100644
--- a/cli/tools/fmt.rs
+++ b/cli/tools/fmt.rs
@@ -120,7 +120,13 @@ pub async fn format(
             };
           }
 
-          format_files(caches, &fmt_flags, paths_with_options_batches).await?;
+          format_files(
+            caches,
+            cli_options,
+            &fmt_flags,
+            paths_with_options_batches,
+          )
+          .await?;
 
           Ok(())
         })
@@ -133,7 +139,8 @@ pub async fn format(
     let caches = factory.caches()?;
     let paths_with_options_batches =
       resolve_paths_with_options_batches(cli_options, &fmt_flags)?;
-    format_files(caches, &fmt_flags, paths_with_options_batches).await?;
+    format_files(caches, cli_options, &fmt_flags, paths_with_options_batches)
+      .await?;
   }
 
   Ok(())
@@ -172,6 +179,7 @@ fn resolve_paths_with_options_batches(
 
 async fn format_files(
   caches: &Arc<Caches>,
+  cli_options: &Arc<CliOptions>,
   fmt_flags: &FmtFlags,
   paths_with_options_batches: Vec<PathsWithOptions>,
 ) -> Result<(), AnyError> {
@@ -199,6 +207,7 @@ async fn format_files(
         fmt_options.options,
         fmt_options.unstable,
         incremental_cache.clone(),
+        cli_options.ext_flag().clone(),
       )
       .await?;
     incremental_cache.wait_completion().await;
@@ -211,11 +220,16 @@ fn collect_fmt_files(
   cli_options: &CliOptions,
   files: FilePatterns,
 ) -> Result<Vec<PathBuf>, AnyError> {
-  FileCollector::new(|e| is_supported_ext_fmt(e.path))
-    .ignore_git_folder()
-    .ignore_node_modules()
-    .set_vendor_folder(cli_options.vendor_dir_path().map(ToOwned::to_owned))
-    .collect_file_patterns(&deno_config::fs::RealDenoConfigFs, files)
+  FileCollector::new(|e| {
+    cli_options.ext_flag().as_ref().is_some_and(|ext| {
+      is_supported_ext_fmt(Path::new(&format!("placeholder.{ext}")))
+    }) || is_supported_ext_fmt(e.path)
+      || e.path.extension().is_none()
+  })
+  .ignore_git_folder()
+  .ignore_node_modules()
+  .set_vendor_folder(cli_options.vendor_dir_path().map(ToOwned::to_owned))
+  .collect_file_patterns(&deno_config::fs::RealDenoConfigFs, files)
 }
 
 /// Formats markdown (using <https://github.com/dprint/dprint-plugin-markdown>) and its code blocks
@@ -449,8 +463,11 @@ pub fn format_file(
   file_text: &str,
   fmt_options: &FmtOptionsConfig,
   unstable_options: &UnstableFmtOptions,
+  ext: Option<String>,
 ) -> Result<Option<String>, AnyError> {
-  let ext = get_extension(file_path).unwrap_or_default();
+  let ext = ext
+    .or_else(|| get_extension(file_path))
+    .unwrap_or("ts".to_string());
 
   match ext.as_str() {
     "md" | "mkd" | "mkdn" | "mdwn" | "mdown" | "markdown" => {
@@ -493,14 +510,14 @@ pub fn format_file(
     "ipynb" => dprint_plugin_jupyter::format_text(
       file_text,
       |file_path: &Path, file_text: String| {
-        format_file(file_path, &file_text, fmt_options, unstable_options)
+        format_file(file_path, &file_text, fmt_options, unstable_options, None)
       },
     ),
     _ => {
       let config = get_resolved_typescript_config(fmt_options);
       dprint_plugin_typescript::format_text(
         file_path,
-        None,
+        Some(&ext),
         file_text.to_string(),
         &config,
       )
@@ -526,6 +543,7 @@ trait Formatter {
     fmt_options: FmtOptionsConfig,
     unstable_options: UnstableFmtOptions,
     incremental_cache: Arc<IncrementalCache>,
+    ext: Option<String>,
   ) -> Result<(), AnyError>;
 
   fn finish(&self) -> Result<(), AnyError>;
@@ -545,6 +563,7 @@ impl Formatter for CheckFormatter {
     fmt_options: FmtOptionsConfig,
     unstable_options: UnstableFmtOptions,
     incremental_cache: Arc<IncrementalCache>,
+    ext: Option<String>,
   ) -> Result<(), AnyError> {
     // prevent threads outputting at the same time
     let output_lock = Arc::new(Mutex::new(0));
@@ -566,6 +585,7 @@ impl Formatter for CheckFormatter {
           &file_text,
           &fmt_options,
           &unstable_options,
+          ext.clone(),
         ) {
           Ok(Some(formatted_text)) => {
             not_formatted_files_count.fetch_add(1, Ordering::Relaxed);
@@ -643,6 +663,7 @@ impl Formatter for RealFormatter {
     fmt_options: FmtOptionsConfig,
     unstable_options: UnstableFmtOptions,
     incremental_cache: Arc<IncrementalCache>,
+    ext: Option<String>,
   ) -> Result<(), AnyError> {
     let output_lock = Arc::new(Mutex::new(0)); // prevent threads outputting at the same time
 
@@ -662,7 +683,13 @@ impl Formatter for RealFormatter {
           &file_path,
           &file_contents.text,
           |file_path, file_text| {
-            format_file(file_path, file_text, &fmt_options, &unstable_options)
+            format_file(
+              file_path,
+              file_text,
+              &fmt_options,
+              &unstable_options,
+              ext.clone(),
+            )
           },
         ) {
           Ok(Some(formatted_text)) => {
@@ -788,6 +815,7 @@ fn format_stdin(
     &source,
     &fmt_options.options,
     &fmt_options.unstable,
+    None,
   )?;
   if fmt_flags.check {
     #[allow(clippy::print_stdout)]
@@ -1269,6 +1297,7 @@ mod test {
         ..Default::default()
       },
       &UnstableFmtOptions::default(),
+      None,
     )
     .unwrap()
     .unwrap();
diff --git a/cli/tools/lint/linter.rs b/cli/tools/lint/linter.rs
index 777fe4d09..2c2bc43ac 100644
--- a/cli/tools/lint/linter.rs
+++ b/cli/tools/lint/linter.rs
@@ -94,9 +94,16 @@ impl CliLinter {
     &self,
     file_path: &Path,
     source_code: String,
+    ext: Option<&str>,
   ) -> Result<(ParsedSource, Vec<LintDiagnostic>), AnyError> {
     let specifier = specifier_from_file_path(file_path)?;
-    let media_type = MediaType::from_specifier(&specifier);
+    let media_type = if let Some(ext) = ext {
+      MediaType::from_str(&format!("placeholder.{ext}"))
+    } else if file_path.extension().is_none() {
+      MediaType::TypeScript
+    } else {
+      MediaType::from_specifier(&specifier)
+    };
 
     if self.fix {
       self.lint_file_and_fix(&specifier, media_type, source_code, file_path)
diff --git a/cli/tools/lint/mod.rs b/cli/tools/lint/mod.rs
index d5d174bf7..a52d4e462 100644
--- a/cli/tools/lint/mod.rs
+++ b/cli/tools/lint/mod.rs
@@ -117,6 +117,7 @@ pub async fn lint(
           for paths_with_options in paths_with_options_batches {
             linter
               .lint_files(
+                cli_options,
                 paths_with_options.options,
                 lint_config.clone(),
                 paths_with_options.dir,
@@ -155,7 +156,7 @@ pub async fn lint(
           start_dir.maybe_deno_json().map(|c| c.as_ref()),
         )?;
       let mut file_path = cli_options.initial_cwd().join(STDIN_FILE_NAME);
-      if let Some(ext) = &lint_flags.ext {
+      if let Some(ext) = cli_options.ext_flag() {
         file_path.set_extension(ext);
       }
       let r = lint_stdin(&file_path, lint_rules, deno_lint_config);
@@ -179,6 +180,7 @@ pub async fn lint(
       for paths_with_options in paths_with_options_batches {
         linter
           .lint_files(
+            cli_options,
             paths_with_options.options,
             deno_lint_config.clone(),
             paths_with_options.dir,
@@ -264,6 +266,7 @@ impl WorkspaceLinter {
 
   pub async fn lint_files(
     &mut self,
+    cli_options: &Arc<CliOptions>,
     lint_options: LintOptions,
     lint_config: LintConfig,
     member_dir: WorkspaceDirectory,
@@ -348,6 +351,7 @@ impl WorkspaceLinter {
       let reporter_lock = self.reporter_lock.clone();
       let maybe_incremental_cache = maybe_incremental_cache.clone();
       let linter = linter.clone();
+      let cli_options = cli_options.clone();
       async move {
         run_parallelized(paths, {
           move |file_path| {
@@ -361,7 +365,11 @@ impl WorkspaceLinter {
               }
             }
 
-            let r = linter.lint_file(&file_path, file_text);
+            let r = linter.lint_file(
+              &file_path,
+              file_text,
+              cli_options.ext_flag().as_deref(),
+            );
             if let Ok((file_source, file_diagnostics)) = &r {
               if let Some(incremental_cache) = &maybe_incremental_cache {
                 if file_diagnostics.is_empty() {
@@ -421,11 +429,16 @@ fn collect_lint_files(
   cli_options: &CliOptions,
   files: FilePatterns,
 ) -> Result<Vec<PathBuf>, AnyError> {
-  FileCollector::new(|e| is_script_ext(e.path))
-    .ignore_git_folder()
-    .ignore_node_modules()
-    .set_vendor_folder(cli_options.vendor_dir_path().map(ToOwned::to_owned))
-    .collect_file_patterns(&deno_config::fs::RealDenoConfigFs, files)
+  FileCollector::new(|e| {
+    cli_options.ext_flag().as_ref().is_some_and(|ext| {
+      is_script_ext(Path::new(&format!("placeholder.{ext}")))
+    }) || is_script_ext(e.path)
+      || e.path.extension().is_none()
+  })
+  .ignore_git_folder()
+  .ignore_node_modules()
+  .set_vendor_folder(cli_options.vendor_dir_path().map(ToOwned::to_owned))
+  .collect_file_patterns(&deno_config::fs::RealDenoConfigFs, files)
 }
 
 #[allow(clippy::print_stdout)]
@@ -497,7 +510,7 @@ fn lint_stdin(
   });
 
   linter
-    .lint_file(file_path, deno_ast::strip_bom(source_code))
+    .lint_file(file_path, deno_ast::strip_bom(source_code), None)
     .map_err(AnyError::from)
 }
 
diff --git a/cli/tools/registry/pm/cache_deps.rs b/cli/tools/registry/pm/cache_deps.rs
index a03c30df8..a59817055 100644
--- a/cli/tools/registry/pm/cache_deps.rs
+++ b/cli/tools/registry/pm/cache_deps.rs
@@ -107,6 +107,7 @@ pub async fn cache_top_level_deps(
         false,
         deno_config::deno_json::TsTypeLib::DenoWorker,
         crate::file_fetcher::FetchPermissionsOption::AllowAll,
+        None,
       )
       .await?;
   }
diff --git a/cli/tools/test/mod.rs b/cli/tools/test/mod.rs
index d043ffcba..e81abad0b 100644
--- a/cli/tools/test/mod.rs
+++ b/cli/tools/test/mod.rs
@@ -1583,7 +1583,10 @@ pub async fn run_tests(
 
   // Typecheck
   main_graph_container
-    .check_specifiers(&specifiers_for_typecheck_and_test)
+    .check_specifiers(
+      &specifiers_for_typecheck_and_test,
+      cli_options.ext_flag().as_ref(),
+    )
     .await?;
 
   if workspace_test_options.no_run {
@@ -1757,7 +1760,10 @@ pub async fn run_tests_with_watch(
 
         // Typecheck
         main_graph_container
-          .check_specifiers(&specifiers_for_typecheck_and_test)
+          .check_specifiers(
+            &specifiers_for_typecheck_and_test,
+            cli_options.ext_flag().as_ref(),
+          )
           .await?;
 
         if workspace_test_options.no_run {
diff --git a/tests/integration/run_tests.rs b/tests/integration/run_tests.rs
index 50f0f58f8..6b0901e26 100644
--- a/tests/integration/run_tests.rs
+++ b/tests/integration/run_tests.rs
@@ -148,11 +148,6 @@ itest!(_021_mjs_modules {
   output: "run/021_mjs_modules.ts.out",
 });
 
-itest!(_023_no_ext {
-  args: "run --reload --check run/023_no_ext",
-  output: "run/023_no_ext.out",
-});
-
 itest!(_025_reload_js_type_error {
   args: "run --quiet --reload run/025_reload_js_type_error.js",
   output: "run/025_reload_js_type_error.js.out",
@@ -4209,12 +4204,6 @@ itest!(error_cause_recursive {
   exit_code: 1,
 });
 
-itest!(default_file_extension_is_js {
-  args: "run --check file_extensions/js_without_extension",
-  output: "file_extensions/js_without_extension.out",
-  exit_code: 0,
-});
-
 itest!(js_without_extension {
   args: "run --ext js --check file_extensions/js_without_extension",
   output: "file_extensions/js_without_extension.out",
diff --git a/tests/specs/bench/default_ts/__test__.jsonc b/tests/specs/bench/default_ts/__test__.jsonc
new file mode 100644
index 000000000..a5657290d
--- /dev/null
+++ b/tests/specs/bench/default_ts/__test__.jsonc
@@ -0,0 +1,13 @@
+{
+  "tempDir": true,
+  "tests": {
+    "ext_flag": {
+      "args": "bench --ext=ts as_ts.js",
+      "output": "ext.out"
+    },
+    "extensionless": {
+      "args": "bench extensionless",
+      "output": "extensionless.out"
+    }
+  }
+}
diff --git a/tests/specs/bench/default_ts/as_ts.js b/tests/specs/bench/default_ts/as_ts.js
new file mode 100644
index 000000000..914439a9f
--- /dev/null
+++ b/tests/specs/bench/default_ts/as_ts.js
@@ -0,0 +1,3 @@
+Deno.bench(function foo() {
+  const x: string = "foo";
+});
diff --git a/tests/specs/bench/default_ts/ext.out b/tests/specs/bench/default_ts/ext.out
new file mode 100644
index 000000000..be4e34aac
--- /dev/null
+++ b/tests/specs/bench/default_ts/ext.out
@@ -0,0 +1,5 @@
+Check file:///[WILDCARD]/as_ts.js
+[WILDCARD]
+
+file:///[WILDCARD]/as_ts.js
+[WILDCARD]
diff --git a/tests/specs/bench/default_ts/extensionless b/tests/specs/bench/default_ts/extensionless
new file mode 100644
index 000000000..914439a9f
--- /dev/null
+++ b/tests/specs/bench/default_ts/extensionless
@@ -0,0 +1,3 @@
+Deno.bench(function foo() {
+  const x: string = "foo";
+});
diff --git a/tests/specs/bench/default_ts/extensionless.out b/tests/specs/bench/default_ts/extensionless.out
new file mode 100644
index 000000000..e9442310e
--- /dev/null
+++ b/tests/specs/bench/default_ts/extensionless.out
@@ -0,0 +1,5 @@
+Check file:///[WILDCARD]/extensionless
+[WILDCARD]
+
+file:///[WILDCARD]/extensionless
+[WILDCARD]
diff --git a/tests/specs/fmt/default_ts/__test__.jsonc b/tests/specs/fmt/default_ts/__test__.jsonc
new file mode 100644
index 000000000..24d77a79e
--- /dev/null
+++ b/tests/specs/fmt/default_ts/__test__.jsonc
@@ -0,0 +1,18 @@
+{
+  "tempDir": true,
+  "tests": {
+    "stdin": {
+      "args": "fmt -",
+      "input": "const x: string = \"foo\";",
+      "output": "const x: string = \"foo\";\n"
+    },
+    "ext_flag": {
+      "args": "fmt --ext=ts as_ts.js",
+      "output": "Checked 1 file\n"
+    },
+    "extensionless": {
+      "args": "fmt extensionless",
+      "output": "Checked 1 file\n"
+    }
+  }
+}
diff --git a/tests/specs/fmt/default_ts/as_ts.js b/tests/specs/fmt/default_ts/as_ts.js
new file mode 100644
index 000000000..72a35c2a8
--- /dev/null
+++ b/tests/specs/fmt/default_ts/as_ts.js
@@ -0,0 +1 @@
+const x: string = "foo";
diff --git a/tests/specs/fmt/default_ts/extensionless b/tests/specs/fmt/default_ts/extensionless
new file mode 100644
index 000000000..72a35c2a8
--- /dev/null
+++ b/tests/specs/fmt/default_ts/extensionless
@@ -0,0 +1 @@
+const x: string = "foo";
diff --git a/tests/specs/lint/default_ts/__test__.jsonc b/tests/specs/lint/default_ts/__test__.jsonc
new file mode 100644
index 000000000..ff0f342ab
--- /dev/null
+++ b/tests/specs/lint/default_ts/__test__.jsonc
@@ -0,0 +1,18 @@
+{
+  "tempDir": true,
+  "tests": {
+    "stdin": {
+      "args": "lint -",
+      "input": "const _x: string = \"foo\";",
+      "output": "Checked 1 file\n"
+    },
+    "ext_flag": {
+      "args": "lint --ext=ts as_ts.js",
+      "output": "Checked 1 file\n"
+    },
+    "extensionless": {
+      "args": "lint extensionless",
+      "output": "Checked 1 file\n"
+    }
+  }
+}
diff --git a/tests/specs/lint/default_ts/as_ts.js b/tests/specs/lint/default_ts/as_ts.js
new file mode 100644
index 000000000..3508e99b6
--- /dev/null
+++ b/tests/specs/lint/default_ts/as_ts.js
@@ -0,0 +1 @@
+const _x: string = "foo";
diff --git a/tests/specs/lint/default_ts/extensionless b/tests/specs/lint/default_ts/extensionless
new file mode 100644
index 000000000..3508e99b6
--- /dev/null
+++ b/tests/specs/lint/default_ts/extensionless
@@ -0,0 +1 @@
+const _x: string = "foo";
diff --git a/tests/specs/mod.rs b/tests/specs/mod.rs
index 9565aa71f..34221dd9d 100644
--- a/tests/specs/mod.rs
+++ b/tests/specs/mod.rs
@@ -176,6 +176,7 @@ struct StepMetaData {
   pub command_name: Option<String>,
   #[serde(default)]
   pub envs: HashMap<String, String>,
+  pub input: Option<String>,
   pub output: String,
   #[serde(default)]
   pub exit_code: i32,
@@ -406,6 +407,10 @@ fn run_step(
     true => command.show_output(),
     false => command,
   };
+  let command = match &step.input {
+    Some(input) => command.stdin_text(input),
+    None => command,
+  };
   let output = command.run();
   if step.output.ends_with(".out") {
     let test_output_path = cwd.join(&step.output);
diff --git a/tests/specs/run/default_ts/__test__.jsonc b/tests/specs/run/default_ts/__test__.jsonc
new file mode 100644
index 000000000..07e3d8336
--- /dev/null
+++ b/tests/specs/run/default_ts/__test__.jsonc
@@ -0,0 +1,18 @@
+{
+  "tempDir": true,
+  "tests": {
+    "stdin": {
+      "args": "run -",
+      "input": "const x: string = \"foo\";console.log(x)",
+      "output": "foo\n"
+    },
+    "ext_flag": {
+      "args": "run --ext=ts as_ts.js",
+      "output": "foo\n"
+    },
+    "extensionless": {
+      "args": "run extensionless",
+      "output": "foo\n"
+    }
+  }
+}
diff --git a/tests/specs/run/default_ts/as_ts.js b/tests/specs/run/default_ts/as_ts.js
new file mode 100644
index 000000000..cef8995bc
--- /dev/null
+++ b/tests/specs/run/default_ts/as_ts.js
@@ -0,0 +1,2 @@
+const x: string = "foo";
+console.log(x);
diff --git a/tests/specs/run/default_ts/extensionless b/tests/specs/run/default_ts/extensionless
new file mode 100644
index 000000000..cef8995bc
--- /dev/null
+++ b/tests/specs/run/default_ts/extensionless
@@ -0,0 +1,2 @@
+const x: string = "foo";
+console.log(x);
diff --git a/tests/specs/test/default_ts/__test__.jsonc b/tests/specs/test/default_ts/__test__.jsonc
new file mode 100644
index 000000000..778fca5c5
--- /dev/null
+++ b/tests/specs/test/default_ts/__test__.jsonc
@@ -0,0 +1,13 @@
+{
+  "tempDir": true,
+  "tests": {
+    "ext_flag": {
+      "args": "test --ext=ts as_ts.js",
+      "output": "ext.out"
+    },
+    "extensionless": {
+      "args": "test extensionless",
+      "output": "extensionless.out"
+    }
+  }
+}
diff --git a/tests/specs/test/default_ts/as_ts.js b/tests/specs/test/default_ts/as_ts.js
new file mode 100644
index 000000000..52cb8eacc
--- /dev/null
+++ b/tests/specs/test/default_ts/as_ts.js
@@ -0,0 +1,3 @@
+Deno.test(function foo() {
+  const x: string = "foo";
+});
diff --git a/tests/specs/test/default_ts/ext.out b/tests/specs/test/default_ts/ext.out
new file mode 100644
index 000000000..55f7526a5
--- /dev/null
+++ b/tests/specs/test/default_ts/ext.out
@@ -0,0 +1,4 @@
+Check file:///[WILDCARD]/as_ts.js
+running 1 test from ./as_ts.js
+[WILDCARD]
+
diff --git a/tests/specs/test/default_ts/extensionless b/tests/specs/test/default_ts/extensionless
new file mode 100644
index 000000000..52cb8eacc
--- /dev/null
+++ b/tests/specs/test/default_ts/extensionless
@@ -0,0 +1,3 @@
+Deno.test(function foo() {
+  const x: string = "foo";
+});
diff --git a/tests/specs/test/default_ts/extensionless.out b/tests/specs/test/default_ts/extensionless.out
new file mode 100644
index 000000000..20d4ee2cb
--- /dev/null
+++ b/tests/specs/test/default_ts/extensionless.out
@@ -0,0 +1,4 @@
+Check file:///[WILDCARD]/extensionless
+running 1 test from ./extensionless
+[WILDCARD]
+
diff --git a/tools/lint.js b/tools/lint.js
index a9f940006..de0db015f 100755
--- a/tools/lint.js
+++ b/tools/lint.js
@@ -218,7 +218,7 @@ async function ensureNoNewITests() {
     "pm_tests.rs": 0,
     "publish_tests.rs": 0,
     "repl_tests.rs": 0,
-    "run_tests.rs": 333,
+    "run_tests.rs": 331,
     "shared_library_tests.rs": 0,
     "task_tests.rs": 4,
     "test_tests.rs": 0,