diff --git a/cli/tools/bench.rs b/cli/tools/bench.rs
index 70fc34ca1f..0aa7cc365c 100644
--- a/cli/tools/bench.rs
+++ b/cli/tools/bench.rs
@@ -691,10 +691,10 @@ pub async fn run_benchmarks_with_watch(
         );
 
         if let Some(changed) = &changed {
-          for path in changed.iter().filter_map(|path| {
-            deno_core::resolve_url_or_path_deprecated(&path.to_string_lossy())
-              .ok()
-          }) {
+          for path in changed
+            .iter()
+            .filter_map(|path| ModuleSpecifier::from_file_path(path).ok())
+          {
             if modules.contains(&path) {
               modules_to_reload.push(specifier);
               break;
diff --git a/cli/tools/bundle.rs b/cli/tools/bundle.rs
index c1d4befb12..5a42f834ea 100644
--- a/cli/tools/bundle.rs
+++ b/cli/tools/bundle.rs
@@ -5,7 +5,7 @@ use std::sync::Arc;
 
 use deno_core::error::AnyError;
 use deno_core::futures::FutureExt;
-use deno_core::resolve_url_or_path_deprecated;
+use deno_core::resolve_url_or_path;
 use deno_graph::Module;
 use deno_runtime::colors;
 
@@ -35,16 +35,17 @@ pub async fn bundle(
     "Use alternative bundlers like \"deno_emit\", \"esbuild\" or \"rollup\" instead."
   );
 
+  let module_specifier =
+    resolve_url_or_path(&bundle_flags.source_file, cli_options.initial_cwd())?;
+
   let resolver = |_| {
     let cli_options = cli_options.clone();
-    let source_file1 = &bundle_flags.source_file;
-    let source_file2 = &bundle_flags.source_file;
+    let module_specifier = &module_specifier;
     async move {
-      let module_specifier = resolve_url_or_path_deprecated(source_file1)?;
-
       log::debug!(">>>>> bundle START");
       let ps = ProcState::from_options(cli_options).await?;
-      let graph = create_graph_and_maybe_check(module_specifier, &ps).await?;
+      let graph =
+        create_graph_and_maybe_check(module_specifier.clone(), &ps).await?;
 
       let mut paths_to_watch: Vec<PathBuf> = graph
         .specifiers()
@@ -74,7 +75,7 @@ pub async fn bundle(
         result: Ok((ps, graph)),
       },
       Err(e) => ResolutionResult::Restart {
-        paths_to_watch: vec![PathBuf::from(source_file2)],
+        paths_to_watch: vec![module_specifier.to_file_path().unwrap()],
         result: Err(e),
       },
     })
diff --git a/cli/tools/run.rs b/cli/tools/run.rs
index 04ddcb4d99..84ec75e1a5 100644
--- a/cli/tools/run.rs
+++ b/cli/tools/run.rs
@@ -9,7 +9,6 @@ use deno_core::anyhow::Context;
 use deno_core::error::AnyError;
 use deno_core::resolve_path;
 use deno_core::resolve_url_or_path;
-use deno_core::resolve_url_or_path_deprecated;
 use deno_graph::npm::NpmPackageReqReference;
 use deno_runtime::permissions::Permissions;
 use deno_runtime::permissions::PermissionsContainer;
@@ -104,10 +103,10 @@ pub async fn run_from_stdin(flags: Flags) -> Result<i32, AnyError> {
 // code properly.
 async fn run_with_watch(flags: Flags, script: String) -> Result<i32, AnyError> {
   let flags = Arc::new(flags);
-  let main_module = resolve_url_or_path_deprecated(&script)?;
   let (sender, receiver) = tokio::sync::mpsc::unbounded_channel();
   let mut ps =
     ProcState::build_for_file_watcher((*flags).clone(), sender.clone()).await?;
+  let main_module = resolve_url_or_path(&script, ps.options.initial_cwd())?;
 
   let operation = |main_module: ModuleSpecifier| {
     ps.reset_for_file_watcher();
diff --git a/cli/tools/test.rs b/cli/tools/test.rs
index 12f5d7c1f9..d200a30298 100644
--- a/cli/tools/test.rs
+++ b/cli/tools/test.rs
@@ -740,6 +740,7 @@ async fn test_specifier(
 }
 
 fn extract_files_from_regex_blocks(
+  current_dir: &Path,
   specifier: &ModuleSpecifier,
   source: &str,
   media_type: MediaType,
@@ -799,13 +800,16 @@ fn extract_files_from_regex_blocks(
         writeln!(file_source, "{}", text.as_str()).unwrap();
       }
 
-      let file_specifier = deno_core::resolve_url_or_path_deprecated(&format!(
-        "{}${}-{}{}",
-        specifier,
-        file_line_index + line_offset + 1,
-        file_line_index + line_offset + line_count + 1,
-        file_media_type.as_ts_extension(),
-      ))
+      let file_specifier = deno_core::resolve_url_or_path(
+        &format!(
+          "{}${}-{}{}",
+          specifier,
+          file_line_index + line_offset + 1,
+          file_line_index + line_offset + line_count + 1,
+          file_media_type.as_ts_extension(),
+        ),
+        current_dir,
+      )
       .unwrap();
 
       Some(File {
@@ -823,6 +827,7 @@ fn extract_files_from_regex_blocks(
 }
 
 fn extract_files_from_source_comments(
+  current_dir: &Path,
   specifier: &ModuleSpecifier,
   source: Arc<str>,
   media_type: MediaType,
@@ -850,6 +855,7 @@ fn extract_files_from_source_comments(
     })
     .flat_map(|comment| {
       extract_files_from_regex_blocks(
+        current_dir,
         specifier,
         &comment.text,
         media_type,
@@ -865,6 +871,7 @@ fn extract_files_from_source_comments(
 }
 
 fn extract_files_from_fenced_blocks(
+  current_dir: &Path,
   specifier: &ModuleSpecifier,
   source: &str,
   media_type: MediaType,
@@ -878,6 +885,7 @@ fn extract_files_from_fenced_blocks(
   let lines_regex = Regex::new(r"(?:\# ?)?(.*)")?;
 
   extract_files_from_regex_blocks(
+    current_dir,
     specifier,
     source,
     media_type,
@@ -898,12 +906,14 @@ async fn fetch_inline_files(
 
     let inline_files = if file.media_type == MediaType::Unknown {
       extract_files_from_fenced_blocks(
+        ps.options.initial_cwd(),
         &file.specifier,
         &file.source,
         file.media_type,
       )
     } else {
       extract_files_from_source_comments(
+        ps.options.initial_cwd(),
         &file.specifier,
         file.source,
         file.media_type,
@@ -1427,10 +1437,10 @@ pub async fn run_tests_with_watch(
         );
 
         if let Some(changed) = &changed {
-          for path in changed.iter().filter_map(|path| {
-            deno_core::resolve_url_or_path_deprecated(&path.to_string_lossy())
-              .ok()
-          }) {
+          for path in changed
+            .iter()
+            .filter_map(|path| ModuleSpecifier::from_file_path(path).ok())
+          {
             if modules.contains(&path) {
               modules_to_reload.push(specifier);
               break;