Merge branch 'denoland:main' into main

6 files changed, 1965 insertions, 432 deletions

diff --git a/cli/standalone/binary.rs b/cli/standalone/binary.rs
index 1290a238f..37753bafc 100644
--- a/cli/standalone/binary.rs
+++ b/cli/standalone/binary.rs
@@ -9,14 +9,19 @@ use std::ffi::OsString;
 use std::fs;
 use std::fs::File;
 use std::future::Future;
+use std::io::ErrorKind;
 use std::io::Read;
 use std::io::Seek;
 use std::io::SeekFrom;
 use std::io::Write;
+use std::ops::Range;
 use std::path::Path;
 use std::path::PathBuf;
 use std::process::Command;
+use std::sync::Arc;
 
+use deno_ast::MediaType;
+use deno_ast::ModuleKind;
 use deno_ast::ModuleSpecifier;
 use deno_config::workspace::PackageJsonDepResolution;
 use deno_config::workspace::ResolverWorkspaceJsrPackage;
@@ -30,13 +35,23 @@ use deno_core::futures::AsyncReadExt;
 use deno_core::futures::AsyncSeekExt;
 use deno_core::serde_json;
 use deno_core::url::Url;
+use deno_graph::source::RealFileSystem;
+use deno_graph::ModuleGraph;
+use deno_npm::resolution::SerializedNpmResolutionSnapshot;
+use deno_npm::resolution::SerializedNpmResolutionSnapshotPackage;
+use deno_npm::resolution::ValidSerializedNpmResolutionSnapshot;
+use deno_npm::NpmPackageId;
 use deno_npm::NpmSystemInfo;
+use deno_runtime::deno_fs;
+use deno_runtime::deno_fs::FileSystem;
+use deno_runtime::deno_fs::RealFs;
+use deno_runtime::deno_io::fs::FsError;
 use deno_runtime::deno_node::PackageJson;
+use deno_runtime::ops::otel::OtelConfig;
 use deno_semver::npm::NpmVersionReqParseError;
 use deno_semver::package::PackageReq;
 use deno_semver::Version;
 use deno_semver::VersionReqSpecifierParseError;
-use eszip::EszipRelativeFileBaseUrl;
 use indexmap::IndexMap;
 use log::Level;
 use serde::Deserialize;
@@ -49,10 +64,13 @@ use crate::args::NpmInstallDepsProvider;
 use crate::args::PermissionFlags;
 use crate::args::UnstableConfig;
 use crate::cache::DenoDir;
+use crate::cache::FastInsecureHasher;
+use crate::emit::Emitter;
 use crate::file_fetcher::FileFetcher;
 use crate::http_util::HttpClientProvider;
 use crate::npm::CliNpmResolver;
 use crate::npm::InnerCliNpmResolverRef;
+use crate::resolver::CjsTracker;
 use crate::shared::ReleaseChannel;
 use crate::standalone::virtual_fs::VfsEntry;
 use crate::util::archive;
@@ -60,12 +78,63 @@ use crate::util::fs::canonicalize_path_maybe_not_exists;
 use crate::util::progress_bar::ProgressBar;
 use crate::util::progress_bar::ProgressBarStyle;
 
+use super::file_system::DenoCompileFileSystem;
+use super::serialization::deserialize_binary_data_section;
+use super::serialization::serialize_binary_data_section;
+use super::serialization::DenoCompileModuleData;
+use super::serialization::DeserializedDataSection;
+use super::serialization::RemoteModulesStore;
+use super::serialization::RemoteModulesStoreBuilder;
 use super::virtual_fs::FileBackedVfs;
 use super::virtual_fs::VfsBuilder;
 use super::virtual_fs::VfsRoot;
 use super::virtual_fs::VirtualDirectory;
 
-const MAGIC_TRAILER: &[u8; 8] = b"d3n0l4nd";
+/// A URL that can be designated as the base for relative URLs.
+///
+/// After creation, this URL may be used to get the key for a
+/// module in the binary.
+#[derive(Debug, Clone, Copy, PartialEq, Eq, Hash)]
+pub struct StandaloneRelativeFileBaseUrl<'a>(&'a Url);
+
+impl<'a> From<&'a Url> for StandaloneRelativeFileBaseUrl<'a> {
+  fn from(url: &'a Url) -> Self {
+    Self(url)
+  }
+}
+
+impl<'a> StandaloneRelativeFileBaseUrl<'a> {
+  pub fn new(url: &'a Url) -> Self {
+    debug_assert_eq!(url.scheme(), "file");
+    Self(url)
+  }
+
+  /// Gets the module map key of the provided specifier.
+  ///
+  /// * Descendant file specifiers will be made relative to the base.
+  /// * Non-descendant file specifiers will stay as-is (absolute).
+  /// * Non-file specifiers will stay as-is.
+  pub fn specifier_key<'b>(&self, target: &'b Url) -> Cow<'b, str> {
+    if target.scheme() != "file" {
+      return Cow::Borrowed(target.as_str());
+    }
+
+    match self.0.make_relative(target) {
+      Some(relative) => {
+        if relative.starts_with("../") {
+          Cow::Borrowed(target.as_str())
+        } else {
+          Cow::Owned(relative)
+        }
+      }
+      None => Cow::Borrowed(target.as_str()),
+    }
+  }
+
+  pub fn inner(&self) -> &Url {
+    self.0
+  }
+}
 
 #[derive(Deserialize, Serialize)]
 pub enum NodeModules {
@@ -106,6 +175,7 @@ pub struct SerializedWorkspaceResolver {
 pub struct Metadata {
   pub argv: Vec<String>,
   pub seed: Option<u64>,
+  pub code_cache_key: Option<u64>,
   pub permissions: PermissionFlags,
   pub location: Option<Url>,
   pub v8_flags: Vec<String>,
@@ -118,80 +188,26 @@ pub struct Metadata {
   pub entrypoint_key: String,
   pub node_modules: Option<NodeModules>,
   pub unstable_config: UnstableConfig,
-}
-
-pub fn load_npm_vfs(root_dir_path: PathBuf) -> Result<FileBackedVfs, AnyError> {
-  let data = libsui::find_section("d3n0l4nd").unwrap();
-
-  // We do the first part sync so it can complete quickly
-  let trailer: [u8; TRAILER_SIZE] = data[0..TRAILER_SIZE].try_into().unwrap();
-  let trailer = match Trailer::parse(&trailer)? {
-    None => panic!("Could not find trailer"),
-    Some(trailer) => trailer,
-  };
-  let data = &data[TRAILER_SIZE..];
-
-  let vfs_data =
-    &data[trailer.npm_vfs_pos as usize..trailer.npm_files_pos as usize];
-  let mut dir: VirtualDirectory = serde_json::from_slice(vfs_data)?;
-
-  // align the name of the directory with the root dir
-  dir.name = root_dir_path
-    .file_name()
-    .unwrap()
-    .to_string_lossy()
-    .to_string();
-
-  let fs_root = VfsRoot {
-    dir,
-    root_path: root_dir_path,
-    start_file_offset: trailer.npm_files_pos,
-  };
-  Ok(FileBackedVfs::new(data.to_vec(), fs_root))
+  pub otel_config: Option<OtelConfig>, // None means disabled.
 }
 
 fn write_binary_bytes(
   mut file_writer: File,
   original_bin: Vec<u8>,
   metadata: &Metadata,
-  eszip: eszip::EszipV2,
-  npm_vfs: Option<&VirtualDirectory>,
-  npm_files: &Vec<Vec<u8>>,
+  npm_snapshot: Option<SerializedNpmResolutionSnapshot>,
+  remote_modules: &RemoteModulesStoreBuilder,
+  vfs: VfsBuilder,
   compile_flags: &CompileFlags,
 ) -> Result<(), AnyError> {
-  let metadata = serde_json::to_string(metadata)?.as_bytes().to_vec();
-  let npm_vfs = serde_json::to_string(&npm_vfs)?.as_bytes().to_vec();
-  let eszip_archive = eszip.into_bytes();
-
-  let mut writer = Vec::new();
-
-  // write the trailer, which includes the positions
-  // of the data blocks in the file
-  writer.write_all(&{
-    let metadata_pos = eszip_archive.len() as u64;
-    let npm_vfs_pos = metadata_pos + (metadata.len() as u64);
-    let npm_files_pos = npm_vfs_pos + (npm_vfs.len() as u64);
-    Trailer {
-      eszip_pos: 0,
-      metadata_pos,
-      npm_vfs_pos,
-      npm_files_pos,
-    }
-    .as_bytes()
-  })?;
-
-  writer.write_all(&eszip_archive)?;
-  writer.write_all(&metadata)?;
-  writer.write_all(&npm_vfs)?;
-  for file in npm_files {
-    writer.write_all(file)?;
-  }
+  let data_section_bytes =
+    serialize_binary_data_section(metadata, npm_snapshot, remote_modules, vfs)?;
 
   let target = compile_flags.resolve_target();
   if target.contains("linux") {
     libsui::Elf::new(&original_bin).append(
       "d3n0l4nd",
-      &writer,
+      &data_section_bytes,
       &mut file_writer,
     )?;
   } else if target.contains("windows") {
@@ -201,11 +217,11 @@ fn write_binary_bytes(
       pe = pe.set_icon(&icon)?;
     }
 
-    pe.write_resource("d3n0l4nd", writer)?
+    pe.write_resource("d3n0l4nd", data_section_bytes)?
       .build(&mut file_writer)?;
   } else if target.contains("darwin") {
     libsui::Macho::from(original_bin)?
-      .write_section("d3n0l4nd", writer)?
+      .write_section("d3n0l4nd", data_section_bytes)?
       .build_and_sign(&mut file_writer)?;
   }
   Ok(())
@@ -221,6 +237,67 @@ pub fn is_standalone_binary(exe_path: &Path) -> bool {
     || libsui::utils::is_macho(&data)
 }
 
+pub struct StandaloneData {
+  pub fs: Arc<dyn deno_fs::FileSystem>,
+  pub metadata: Metadata,
+  pub modules: StandaloneModules,
+  pub npm_snapshot: Option<ValidSerializedNpmResolutionSnapshot>,
+  pub root_path: PathBuf,
+  pub vfs: Arc<FileBackedVfs>,
+}
+
+pub struct StandaloneModules {
+  remote_modules: RemoteModulesStore,
+  vfs: Arc<FileBackedVfs>,
+}
+
+impl StandaloneModules {
+  pub fn resolve_specifier<'a>(
+    &'a self,
+    specifier: &'a ModuleSpecifier,
+  ) -> Result<Option<&'a ModuleSpecifier>, AnyError> {
+    if specifier.scheme() == "file" {
+      Ok(Some(specifier))
+    } else {
+      self.remote_modules.resolve_specifier(specifier)
+    }
+  }
+
+  pub fn has_file(&self, path: &Path) -> bool {
+    self.vfs.file_entry(path).is_ok()
+  }
+
+  pub fn read<'a>(
+    &'a self,
+    specifier: &'a ModuleSpecifier,
+  ) -> Result<Option<DenoCompileModuleData<'a>>, AnyError> {
+    if specifier.scheme() == "file" {
+      let path = deno_path_util::url_to_file_path(specifier)?;
+      let bytes = match self.vfs.file_entry(&path) {
+        Ok(entry) => self.vfs.read_file_all(entry)?,
+        Err(err) if err.kind() == ErrorKind::NotFound => {
+          let bytes = match RealFs.read_file_sync(&path, None) {
+            Ok(bytes) => bytes,
+            Err(FsError::Io(err)) if err.kind() == ErrorKind::NotFound => {
+              return Ok(None)
+            }
+            Err(err) => return Err(err.into()),
+          };
+          Cow::Owned(bytes)
+        }
+        Err(err) => return Err(err.into()),
+      };
+      Ok(Some(DenoCompileModuleData {
+        media_type: MediaType::from_specifier(specifier),
+        specifier,
+        data: bytes,
+      }))
+    } else {
+      self.remote_modules.read(specifier)
+    }
+  }
+}
+
 /// This function will try to run this binary as a standalone binary
 /// produced by `deno compile`. It determines if this is a standalone
 /// binary by skipping over the trailer width at the end of the file,
@@ -228,110 +305,67 @@ pub fn is_standalone_binary(exe_path: &Path) -> bool {
 /// the bundle is executed. If not, this function exits with `Ok(None)`.
 pub fn extract_standalone(
   cli_args: Cow<Vec<OsString>>,
-) -> Result<
-  Option<impl Future<Output = Result<(Metadata, eszip::EszipV2), AnyError>>>,
-  AnyError,
-> {
+) -> Result<Option<StandaloneData>, AnyError> {
   let Some(data) = libsui::find_section("d3n0l4nd") else {
     return Ok(None);
   };
 
-  // We do the first part sync so it can complete quickly
-  let trailer = match Trailer::parse(&data[0..TRAILER_SIZE])? {
+  let DeserializedDataSection {
+    mut metadata,
+    npm_snapshot,
+    remote_modules,
+    mut vfs_dir,
+    vfs_files_data,
+  } = match deserialize_binary_data_section(data)? {
+    Some(data_section) => data_section,
     None => return Ok(None),
-    Some(trailer) => trailer,
   };
 
+  let root_path = {
+    let maybe_current_exe = std::env::current_exe().ok();
+    let current_exe_name = maybe_current_exe
+      .as_ref()
+      .and_then(|p| p.file_name())
+      .map(|p| p.to_string_lossy())
+      // should never happen
+      .unwrap_or_else(|| Cow::Borrowed("binary"));
+    std::env::temp_dir().join(format!("deno-compile-{}", current_exe_name))
+  };
   let cli_args = cli_args.into_owned();
-  // If we have an eszip, read it out
-  Ok(Some(async move {
-    let bufreader =
-      deno_core::futures::io::BufReader::new(&data[TRAILER_SIZE..]);
-
-    let (eszip, loader) = eszip::EszipV2::parse(bufreader)
-      .await
-      .context("Failed to parse eszip header")?;
-
-    let bufreader = loader.await.context("Failed to parse eszip archive")?;
-
-    let mut metadata = String::new();
-
-    bufreader
-      .take(trailer.metadata_len())
-      .read_to_string(&mut metadata)
-      .await
-      .context("Failed to read metadata from the current executable")?;
-
-    let mut metadata: Metadata = serde_json::from_str(&metadata).unwrap();
-    metadata.argv.reserve(cli_args.len() - 1);
-    for arg in cli_args.into_iter().skip(1) {
-      metadata.argv.push(arg.into_string().unwrap());
-    }
-
-    Ok((metadata, eszip))
-  }))
-}
-
-const TRAILER_SIZE: usize = std::mem::size_of::<Trailer>() + 8; // 8 bytes for the magic trailer string
-
-struct Trailer {
-  eszip_pos: u64,
-  metadata_pos: u64,
-  npm_vfs_pos: u64,
-  npm_files_pos: u64,
-}
-
-impl Trailer {
-  pub fn parse(trailer: &[u8]) -> Result<Option<Trailer>, AnyError> {
-    let (magic_trailer, rest) = trailer.split_at(8);
-    if magic_trailer != MAGIC_TRAILER {
-      return Ok(None);
-    }
-
-    let (eszip_archive_pos, rest) = rest.split_at(8);
-    let (metadata_pos, rest) = rest.split_at(8);
-    let (npm_vfs_pos, npm_files_pos) = rest.split_at(8);
-    let eszip_archive_pos = u64_from_bytes(eszip_archive_pos)?;
-    let metadata_pos = u64_from_bytes(metadata_pos)?;
-    let npm_vfs_pos = u64_from_bytes(npm_vfs_pos)?;
-    let npm_files_pos = u64_from_bytes(npm_files_pos)?;
-    Ok(Some(Trailer {
-      eszip_pos: eszip_archive_pos,
-      metadata_pos,
-      npm_vfs_pos,
-      npm_files_pos,
-    }))
-  }
-
-  pub fn metadata_len(&self) -> u64 {
-    self.npm_vfs_pos - self.metadata_pos
-  }
-
-  pub fn npm_vfs_len(&self) -> u64 {
-    self.npm_files_pos - self.npm_vfs_pos
+  metadata.argv.reserve(cli_args.len() - 1);
+  for arg in cli_args.into_iter().skip(1) {
+    metadata.argv.push(arg.into_string().unwrap());
   }
-
-  pub fn as_bytes(&self) -> Vec<u8> {
-    let mut trailer = MAGIC_TRAILER.to_vec();
-    trailer.write_all(&self.eszip_pos.to_be_bytes()).unwrap();
-    trailer.write_all(&self.metadata_pos.to_be_bytes()).unwrap();
-    trailer.write_all(&self.npm_vfs_pos.to_be_bytes()).unwrap();
-    trailer
-      .write_all(&self.npm_files_pos.to_be_bytes())
-      .unwrap();
-    trailer
-  }
-}
-
-fn u64_from_bytes(arr: &[u8]) -> Result<u64, AnyError> {
-  let fixed_arr: &[u8; 8] = arr
-    .try_into()
-    .context("Failed to convert the buffer into a fixed-size array")?;
-  Ok(u64::from_be_bytes(*fixed_arr))
+  let vfs = {
+    // align the name of the directory with the root dir
+    vfs_dir.name = root_path.file_name().unwrap().to_string_lossy().to_string();
+
+    let fs_root = VfsRoot {
+      dir: vfs_dir,
+      root_path: root_path.clone(),
+      start_file_offset: 0,
+    };
+    Arc::new(FileBackedVfs::new(Cow::Borrowed(vfs_files_data), fs_root))
+  };
+  let fs: Arc<dyn deno_fs::FileSystem> =
+    Arc::new(DenoCompileFileSystem::new(vfs.clone()));
+  Ok(Some(StandaloneData {
+    fs,
+    metadata,
+    modules: StandaloneModules {
+      remote_modules,
+      vfs: vfs.clone(),
+    },
+    npm_snapshot,
+    root_path,
+    vfs,
+  }))
 }
 
 pub struct DenoCompileBinaryWriter<'a> {
+  cjs_tracker: &'a CjsTracker,
   deno_dir: &'a DenoDir,
+  emitter: &'a Emitter,
   file_fetcher: &'a FileFetcher,
   http_client_provider: &'a HttpClientProvider,
   npm_resolver: &'a dyn CliNpmResolver,
@@ -342,7 +376,9 @@ pub struct DenoCompileBinaryWriter<'a> {
 impl<'a> DenoCompileBinaryWriter<'a> {
   #[allow(clippy::too_many_arguments)]
   pub fn new(
+    cjs_tracker: &'a CjsTracker,
     deno_dir: &'a DenoDir,
+    emitter: &'a Emitter,
     file_fetcher: &'a FileFetcher,
     http_client_provider: &'a HttpClientProvider,
     npm_resolver: &'a dyn CliNpmResolver,
@@ -350,7 +386,9 @@ impl<'a> DenoCompileBinaryWriter<'a> {
     npm_system_info: NpmSystemInfo,
   ) -> Self {
     Self {
+      cjs_tracker,
       deno_dir,
+      emitter,
       file_fetcher,
       http_client_provider,
       npm_resolver,
@@ -362,8 +400,8 @@ impl<'a> DenoCompileBinaryWriter<'a> {
   pub async fn write_bin(
     &self,
     writer: File,
-    eszip: eszip::EszipV2,
-    root_dir_url: EszipRelativeFileBaseUrl<'_>,
+    graph: &ModuleGraph,
+    root_dir_url: StandaloneRelativeFileBaseUrl<'_>,
     entrypoint: &ModuleSpecifier,
     compile_flags: &CompileFlags,
     cli_options: &CliOptions,
@@ -390,15 +428,17 @@ impl<'a> DenoCompileBinaryWriter<'a> {
         )
       }
     }
-    self.write_standalone_binary(
-      writer,
-      original_binary,
-      eszip,
-      root_dir_url,
-      entrypoint,
-      cli_options,
-      compile_flags,
-    )
+    self
+      .write_standalone_binary(
+        writer,
+        original_binary,
+        graph,
+        root_dir_url,
+        entrypoint,
+        cli_options,
+        compile_flags,
+      )
+      .await
   }
 
   async fn get_base_binary(
@@ -468,14 +508,18 @@ impl<'a> DenoCompileBinaryWriter<'a> {
       self
         .http_client_provider
         .get_or_create()?
-        .download_with_progress(download_url.parse()?, None, &progress)
+        .download_with_progress_and_retries(
+          download_url.parse()?,
+          None,
+          &progress,
+        )
         .await?
     };
     let bytes = match maybe_bytes {
       Some(bytes) => bytes,
       None => {
         log::info!("Download could not be found, aborting");
-        std::process::exit(1)
+        deno_runtime::exit(1);
       }
     };
 
@@ -489,12 +533,12 @@ impl<'a> DenoCompileBinaryWriter<'a> {
   /// This functions creates a standalone deno binary by appending a bundle
   /// and magic trailer to the currently executing binary.
   #[allow(clippy::too_many_arguments)]
-  fn write_standalone_binary(
+  async fn write_standalone_binary(
     &self,
     writer: File,
     original_bin: Vec<u8>,
-    mut eszip: eszip::EszipV2,
-    root_dir_url: EszipRelativeFileBaseUrl<'_>,
+    graph: &ModuleGraph,
+    root_dir_url: StandaloneRelativeFileBaseUrl<'_>,
     entrypoint: &ModuleSpecifier,
     cli_options: &CliOptions,
     compile_flags: &CompileFlags,
@@ -508,19 +552,17 @@ impl<'a> DenoCompileBinaryWriter<'a> {
       None => None,
     };
     let root_path = root_dir_url.inner().to_file_path().unwrap();
-    let (npm_vfs, npm_files, node_modules) = match self.npm_resolver.as_inner()
+    let (maybe_npm_vfs, node_modules, npm_snapshot) = match self
+      .npm_resolver
+      .as_inner()
     {
       InnerCliNpmResolverRef::Managed(managed) => {
         let snapshot =
           managed.serialized_valid_snapshot_for_system(&self.npm_system_info);
         if !snapshot.as_serialized().packages.is_empty() {
-          let (root_dir, files) = self
-            .build_vfs(&root_path, cli_options)?
-            .into_dir_and_files();
-          eszip.add_npm_snapshot(snapshot);
+          let npm_vfs_builder = self.build_npm_vfs(&root_path, cli_options)?;
           (
-            Some(root_dir),
-            files,
+            Some(npm_vfs_builder),
             Some(NodeModules::Managed {
               node_modules_dir: self.npm_resolver.root_node_modules_path().map(
                 |path| {
@@ -532,18 +574,16 @@ impl<'a> DenoCompileBinaryWriter<'a> {
                 },
               ),
             }),
+            Some(snapshot),
           )
         } else {
-          (None, Vec::new(), None)
+          (None, None, None)
         }
       }
       InnerCliNpmResolverRef::Byonm(resolver) => {
-        let (root_dir, files) = self
-          .build_vfs(&root_path, cli_options)?
-          .into_dir_and_files();
+        let npm_vfs_builder = self.build_npm_vfs(&root_path, cli_options)?;
         (
-          Some(root_dir),
-          files,
+          Some(npm_vfs_builder),
           Some(NodeModules::Byonm {
             root_node_modules_dir: resolver.root_node_modules_path().map(
               |node_modules_dir| {
@@ -556,14 +596,91 @@ impl<'a> DenoCompileBinaryWriter<'a> {
               },
             ),
           }),
+          None,
         )
       }
     };
+    let mut vfs = if let Some(npm_vfs) = maybe_npm_vfs {
+      npm_vfs
+    } else {
+      VfsBuilder::new(root_path.clone())?
+    };
+    let mut remote_modules_store = RemoteModulesStoreBuilder::default();
+    let mut code_cache_key_hasher = if cli_options.code_cache_enabled() {
+      Some(FastInsecureHasher::new_deno_versioned())
+    } else {
+      None
+    };
+    for module in graph.modules() {
+      if module.specifier().scheme() == "data" {
+        continue; // don't store data urls as an entry as they're in the code
+      }
+      if let Some(hasher) = &mut code_cache_key_hasher {
+        if let Some(source) = module.source() {
+          hasher.write(module.specifier().as_str().as_bytes());
+          hasher.write(source.as_bytes());
+        }
+      }
+      let (maybe_source, media_type) = match module {
+        deno_graph::Module::Js(m) => {
+          let source = if m.media_type.is_emittable() {
+            let is_cjs = self.cjs_tracker.is_cjs_with_known_is_script(
+              &m.specifier,
+              m.media_type,
+              m.is_script,
+            )?;
+            let module_kind = ModuleKind::from_is_cjs(is_cjs);
+            let source = self
+              .emitter
+              .emit_parsed_source(
+                &m.specifier,
+                m.media_type,
+                module_kind,
+                &m.source,
+              )
+              .await?;
+            source.into_bytes()
+          } else {
+            m.source.as_bytes().to_vec()
+          };
+          (Some(source), m.media_type)
+        }
+        deno_graph::Module::Json(m) => {
+          (Some(m.source.as_bytes().to_vec()), m.media_type)
+        }
+        deno_graph::Module::Npm(_)
+        | deno_graph::Module::Node(_)
+        | deno_graph::Module::External(_) => (None, MediaType::Unknown),
+      };
+      if module.specifier().scheme() == "file" {
+        let file_path = deno_path_util::url_to_file_path(module.specifier())?;
+        vfs
+          .add_file_with_data(
+            &file_path,
+            match maybe_source {
+              Some(source) => source,
+              None => RealFs.read_file_sync(&file_path, None)?,
+            },
+          )
+          .with_context(|| {
+            format!("Failed adding '{}'", file_path.display())
+          })?;
+      } else if let Some(source) = maybe_source {
+        remote_modules_store.add(module.specifier(), media_type, source);
+      }
+    }
+    remote_modules_store.add_redirects(&graph.redirects);
 
     let env_vars_from_env_file = match cli_options.env_file_name() {
-      Some(env_filename) => {
-        log::info!("{} Environment variables from the file \"{}\" were embedded in the generated executable file", crate::colors::yellow("Warning"), env_filename);
-        get_file_env_vars(env_filename.to_string())?
+      Some(env_filenames) => {
+        let mut aggregated_env_vars = IndexMap::new();
+        for env_filename in env_filenames.iter().rev() {
+          log::info!("{} Environment variables from the file \"{}\" were embedded in the generated executable file", crate::colors::yellow("Warning"), env_filename);
+
+          let env_vars = get_file_env_vars(env_filename.to_string())?;
+          aggregated_env_vars.extend(env_vars);
+        }
+        aggregated_env_vars
       }
       None => Default::default(),
     };
@@ -571,6 +688,7 @@ impl<'a> DenoCompileBinaryWriter<'a> {
     let metadata = Metadata {
       argv: compile_flags.args.clone(),
       seed: cli_options.seed(),
+      code_cache_key: code_cache_key_hasher.map(|h| h.finish()),
       location: cli_options.location_flag().clone(),
       permissions: cli_options.permission_flags().clone(),
       v8_flags: cli_options.v8_flags().clone(),
@@ -625,20 +743,21 @@ impl<'a> DenoCompileBinaryWriter<'a> {
         sloppy_imports: cli_options.unstable_sloppy_imports(),
         features: cli_options.unstable_features(),
       },
+      otel_config: cli_options.otel_config(),
     };
 
     write_binary_bytes(
       writer,
       original_bin,
       &metadata,
-      eszip,
-      npm_vfs.as_ref(),
-      &npm_files,
+      npm_snapshot.map(|s| s.into_serialized()),
+      &remote_modules_store,
+      vfs,
       compile_flags,
     )
   }
 
-  fn build_vfs(
+  fn build_npm_vfs(
     &self,
     root_path: &Path,
     cli_options: &CliOptions,
@@ -659,8 +778,9 @@ impl<'a> DenoCompileBinaryWriter<'a> {
         } else {
           // DO NOT include the user's registry url as it may contain credentials,
           // but also don't make this dependent on the registry url
-          let root_path = npm_resolver.global_cache_root_folder();
-          let mut builder = VfsBuilder::new(root_path)?;
+          let global_cache_root_path = npm_resolver.global_cache_root_path();
+          let mut builder =
+            VfsBuilder::new(global_cache_root_path.to_path_buf())?;
           let mut packages =
             npm_resolver.all_system_packages(&self.npm_system_info);
           packages.sort_by(|a, b| a.id.cmp(&b.id)); // determinism
@@ -670,12 +790,12 @@ impl<'a> DenoCompileBinaryWriter<'a> {
             builder.add_dir_recursive(&folder)?;
           }
 
-          // Flatten all the registries folders into a single "node_modules/localhost" folder
+          // Flatten all the registries folders into a single ".deno_compile_node_modules/localhost" folder
           // that will be used by denort when loading the npm cache. This avoids us exposing
           // the user's private registry information and means we don't have to bother
           // serializing all the different registry config into the binary.
           builder.with_root_dir(|root_dir| {
-            root_dir.name = "node_modules".to_string();
+            root_dir.name = ".deno_compile_node_modules".to_string();
             let mut new_entries = Vec::with_capacity(root_dir.entries.len());
             let mut localhost_entries = IndexMap::new();
             for entry in std::mem::take(&mut root_dir.entries) {
@@ -710,6 +830,8 @@ impl<'a> DenoCompileBinaryWriter<'a> {
             root_dir.entries = new_entries;
           });
 
+          builder.set_new_root_path(root_path.to_path_buf())?;
+
           Ok(builder)
         }
       }
diff --git a/cli/standalone/code_cache.rs b/cli/standalone/code_cache.rs
new file mode 100644
index 000000000..25b490544
--- /dev/null
+++ b/cli/standalone/code_cache.rs
@@ -0,0 +1,514 @@
+// Copyright 2018-2024 the Deno authors. All rights reserved. MIT license.
+
+use std::collections::BTreeMap;
+use std::collections::HashMap;
+use std::io::BufReader;
+use std::io::BufWriter;
+use std::io::Read;
+use std::io::Write;
+use std::path::Path;
+use std::path::PathBuf;
+use std::sync::Arc;
+
+use deno_ast::ModuleSpecifier;
+use deno_core::anyhow::bail;
+use deno_core::error::AnyError;
+use deno_core::parking_lot::Mutex;
+use deno_core::unsync::sync::AtomicFlag;
+use deno_runtime::code_cache::CodeCache;
+use deno_runtime::code_cache::CodeCacheType;
+
+use crate::cache::FastInsecureHasher;
+use crate::util::path::get_atomic_file_path;
+use crate::worker::CliCodeCache;
+
+enum CodeCacheStrategy {
+  FirstRun(FirstRunCodeCacheStrategy),
+  SubsequentRun(SubsequentRunCodeCacheStrategy),
+}
+
+#[derive(Debug, Clone, PartialEq, Eq)]
+pub struct DenoCompileCodeCacheEntry {
+  pub source_hash: u64,
+  pub data: Vec<u8>,
+}
+
+pub struct DenoCompileCodeCache {
+  strategy: CodeCacheStrategy,
+}
+
+impl DenoCompileCodeCache {
+  pub fn new(file_path: PathBuf, cache_key: u64) -> Self {
+    // attempt to deserialize the cache data
+    match deserialize(&file_path, cache_key) {
+      Ok(data) => {
+        log::debug!("Loaded {} code cache entries", data.len());
+        Self {
+          strategy: CodeCacheStrategy::SubsequentRun(
+            SubsequentRunCodeCacheStrategy {
+              is_finished: AtomicFlag::lowered(),
+              data: Mutex::new(data),
+            },
+          ),
+        }
+      }
+      Err(err) => {
+        log::debug!("Failed to deserialize code cache: {:#}", err);
+        Self {
+          strategy: CodeCacheStrategy::FirstRun(FirstRunCodeCacheStrategy {
+            cache_key,
+            file_path,
+            is_finished: AtomicFlag::lowered(),
+            data: Mutex::new(FirstRunCodeCacheData {
+              cache: HashMap::new(),
+              add_count: 0,
+            }),
+          }),
+        }
+      }
+    }
+  }
+}
+
+impl CodeCache for DenoCompileCodeCache {
+  fn get_sync(
+    &self,
+    specifier: &ModuleSpecifier,
+    code_cache_type: CodeCacheType,
+    source_hash: u64,
+  ) -> Option<Vec<u8>> {
+    match &self.strategy {
+      CodeCacheStrategy::FirstRun(strategy) => {
+        if !strategy.is_finished.is_raised() {
+          // we keep track of how many times the cache is requested
+          // then serialize the cache when we get that number of
+          // "set" calls
+          strategy.data.lock().add_count += 1;
+        }
+        None
+      }
+      CodeCacheStrategy::SubsequentRun(strategy) => {
+        if strategy.is_finished.is_raised() {
+          return None;
+        }
+        strategy.take_from_cache(specifier, code_cache_type, source_hash)
+      }
+    }
+  }
+
+  fn set_sync(
+    &self,
+    specifier: ModuleSpecifier,
+    code_cache_type: CodeCacheType,
+    source_hash: u64,
+    bytes: &[u8],
+  ) {
+    match &self.strategy {
+      CodeCacheStrategy::FirstRun(strategy) => {
+        if strategy.is_finished.is_raised() {
+          return;
+        }
+
+        let data_to_serialize = {
+          let mut data = strategy.data.lock();
+          data.cache.insert(
+            (specifier.to_string(), code_cache_type),
+            DenoCompileCodeCacheEntry {
+              source_hash,
+              data: bytes.to_vec(),
+            },
+          );
+          if data.add_count != 0 {
+            data.add_count -= 1;
+          }
+          if data.add_count == 0 {
+            // don't allow using the cache anymore
+            strategy.is_finished.raise();
+            if data.cache.is_empty() {
+              None
+            } else {
+              Some(std::mem::take(&mut data.cache))
+            }
+          } else {
+            None
+          }
+        };
+        if let Some(cache_data) = &data_to_serialize {
+          strategy.write_cache_data(cache_data);
+        }
+      }
+      CodeCacheStrategy::SubsequentRun(_) => {
+        // do nothing
+      }
+    }
+  }
+}
+
+impl CliCodeCache for DenoCompileCodeCache {
+  fn enabled(&self) -> bool {
+    match &self.strategy {
+      CodeCacheStrategy::FirstRun(strategy) => {
+        !strategy.is_finished.is_raised()
+      }
+      CodeCacheStrategy::SubsequentRun(strategy) => {
+        !strategy.is_finished.is_raised()
+      }
+    }
+  }
+
+  fn as_code_cache(self: Arc<Self>) -> Arc<dyn CodeCache> {
+    self
+  }
+}
+
+type CodeCacheKey = (String, CodeCacheType);
+
+struct FirstRunCodeCacheData {
+  cache: HashMap<CodeCacheKey, DenoCompileCodeCacheEntry>,
+  add_count: usize,
+}
+
+struct FirstRunCodeCacheStrategy {
+  cache_key: u64,
+  file_path: PathBuf,
+  is_finished: AtomicFlag,
+  data: Mutex<FirstRunCodeCacheData>,
+}
+
+impl FirstRunCodeCacheStrategy {
+  fn write_cache_data(
+    &self,
+    cache_data: &HashMap<CodeCacheKey, DenoCompileCodeCacheEntry>,
+  ) {
+    let count = cache_data.len();
+    let temp_file = get_atomic_file_path(&self.file_path);
+    match serialize(&temp_file, self.cache_key, cache_data) {
+      Ok(()) => {
+        if let Err(err) = std::fs::rename(&temp_file, &self.file_path) {
+          log::debug!("Failed to rename code cache: {}", err);
+        } else {
+          log::debug!("Serialized {} code cache entries", count);
+        }
+      }
+      Err(err) => {
+        let _ = std::fs::remove_file(&temp_file);
+        log::debug!("Failed to serialize code cache: {}", err);
+      }
+    }
+  }
+}
+
+struct SubsequentRunCodeCacheStrategy {
+  is_finished: AtomicFlag,
+  data: Mutex<HashMap<CodeCacheKey, DenoCompileCodeCacheEntry>>,
+}
+
+impl SubsequentRunCodeCacheStrategy {
+  fn take_from_cache(
+    &self,
+    specifier: &ModuleSpecifier,
+    code_cache_type: CodeCacheType,
+    source_hash: u64,
+  ) -> Option<Vec<u8>> {
+    let mut data = self.data.lock();
+    // todo(dsherret): how to avoid the clone here?
+    let entry = data.remove(&(specifier.to_string(), code_cache_type))?;
+    if entry.source_hash != source_hash {
+      return None;
+    }
+    if data.is_empty() {
+      self.is_finished.raise();
+    }
+    Some(entry.data)
+  }
+}
+
+/// File format:
+/// - <header>
+///   - <cache key>
+///   - <u32: number of entries>
+/// - <[entry length]> - u64 * number of entries
+/// - <[entry]>
+///   - <[u8]: entry data>
+///   - <String: specifier>
+///   - <u8>: code cache type
+///   - <u32: specifier length>
+///   - <u64: source hash>
+///   - <u64: entry data hash>
+fn serialize(
+  file_path: &Path,
+  cache_key: u64,
+  cache: &HashMap<CodeCacheKey, DenoCompileCodeCacheEntry>,
+) -> Result<(), AnyError> {
+  let cache_file = std::fs::OpenOptions::new()
+    .create(true)
+    .truncate(true)
+    .write(true)
+    .open(file_path)?;
+  let mut writer = BufWriter::new(cache_file);
+  serialize_with_writer(&mut writer, cache_key, cache)
+}
+
+fn serialize_with_writer<T: Write>(
+  writer: &mut BufWriter<T>,
+  cache_key: u64,
+  cache: &HashMap<CodeCacheKey, DenoCompileCodeCacheEntry>,
+) -> Result<(), AnyError> {
+  // header
+  writer.write_all(&cache_key.to_le_bytes())?;
+  writer.write_all(&(cache.len() as u32).to_le_bytes())?;
+  // lengths of each entry
+  for ((specifier, _), entry) in cache {
+    let len: u64 =
+      entry.data.len() as u64 + specifier.len() as u64 + 1 + 4 + 8 + 8;
+    writer.write_all(&len.to_le_bytes())?;
+  }
+  // entries
+  for ((specifier, code_cache_type), entry) in cache {
+    writer.write_all(&entry.data)?;
+    writer.write_all(&[match code_cache_type {
+      CodeCacheType::EsModule => 0,
+      CodeCacheType::Script => 1,
+    }])?;
+    writer.write_all(specifier.as_bytes())?;
+    writer.write_all(&(specifier.len() as u32).to_le_bytes())?;
+    writer.write_all(&entry.source_hash.to_le_bytes())?;
+    let hash: u64 = FastInsecureHasher::new_without_deno_version()
+      .write(&entry.data)
+      .finish();
+    writer.write_all(&hash.to_le_bytes())?;
+  }
+
+  writer.flush()?;
+
+  Ok(())
+}
+
+fn deserialize(
+  file_path: &Path,
+  expected_cache_key: u64,
+) -> Result<HashMap<CodeCacheKey, DenoCompileCodeCacheEntry>, AnyError> {
+  let cache_file = std::fs::File::open(file_path)?;
+  let mut reader = BufReader::new(cache_file);
+  deserialize_with_reader(&mut reader, expected_cache_key)
+}
+
+fn deserialize_with_reader<T: Read>(
+  reader: &mut BufReader<T>,
+  expected_cache_key: u64,
+) -> Result<HashMap<CodeCacheKey, DenoCompileCodeCacheEntry>, AnyError> {
+  // it's very important to use this below so that a corrupt cache file
+  // doesn't cause a memory allocation error
+  fn new_vec_sized<T: Clone>(
+    capacity: usize,
+    default_value: T,
+  ) -> Result<Vec<T>, AnyError> {
+    let mut vec = Vec::new();
+    vec.try_reserve(capacity)?;
+    vec.resize(capacity, default_value);
+    Ok(vec)
+  }
+
+  fn try_subtract(a: usize, b: usize) -> Result<usize, AnyError> {
+    if a < b {
+      bail!("Integer underflow");
+    }
+    Ok(a - b)
+  }
+
+  let mut header_bytes = vec![0; 8 + 4];
+  reader.read_exact(&mut header_bytes)?;
+  let actual_cache_key = u64::from_le_bytes(header_bytes[..8].try_into()?);
+  if actual_cache_key != expected_cache_key {
+    // cache bust
+    bail!("Cache key mismatch");
+  }
+  let len = u32::from_le_bytes(header_bytes[8..].try_into()?) as usize;
+  // read the lengths for each entry found in the file
+  let entry_len_bytes_capacity = len * 8;
+  let mut entry_len_bytes = new_vec_sized(entry_len_bytes_capacity, 0)?;
+  reader.read_exact(&mut entry_len_bytes)?;
+  let mut lengths = Vec::new();
+  lengths.try_reserve(len)?;
+  for i in 0..len {
+    let pos = i * 8;
+    lengths.push(
+      u64::from_le_bytes(entry_len_bytes[pos..pos + 8].try_into()?) as usize,
+    );
+  }
+
+  let mut map = HashMap::new();
+  map.try_reserve(len)?;
+  for len in lengths {
+    let mut buffer = new_vec_sized(len, 0)?;
+    reader.read_exact(&mut buffer)?;
+    let entry_data_hash_start_pos = try_subtract(buffer.len(), 8)?;
+    let expected_entry_data_hash =
+      u64::from_le_bytes(buffer[entry_data_hash_start_pos..].try_into()?);
+    let source_hash_start_pos = try_subtract(entry_data_hash_start_pos, 8)?;
+    let source_hash = u64::from_le_bytes(
+      buffer[source_hash_start_pos..entry_data_hash_start_pos].try_into()?,
+    );
+    let specifier_end_pos = try_subtract(source_hash_start_pos, 4)?;
+    let specifier_len = u32::from_le_bytes(
+      buffer[specifier_end_pos..source_hash_start_pos].try_into()?,
+    ) as usize;
+    let specifier_start_pos = try_subtract(specifier_end_pos, specifier_len)?;
+    let specifier = String::from_utf8(
+      buffer[specifier_start_pos..specifier_end_pos].to_vec(),
+    )?;
+    let code_cache_type_pos = try_subtract(specifier_start_pos, 1)?;
+    let code_cache_type = match buffer[code_cache_type_pos] {
+      0 => CodeCacheType::EsModule,
+      1 => CodeCacheType::Script,
+      _ => bail!("Invalid code cache type"),
+    };
+    buffer.truncate(code_cache_type_pos);
+    let actual_entry_data_hash: u64 =
+      FastInsecureHasher::new_without_deno_version()
+        .write(&buffer)
+        .finish();
+    if expected_entry_data_hash != actual_entry_data_hash {
+      bail!("Hash mismatch.")
+    }
+    map.insert(
+      (specifier, code_cache_type),
+      DenoCompileCodeCacheEntry {
+        source_hash,
+        data: buffer,
+      },
+    );
+  }
+
+  Ok(map)
+}
+
+#[cfg(test)]
+mod test {
+  use test_util::TempDir;
+
+  use super::*;
+  use std::fs::File;
+
+  #[test]
+  fn serialize_deserialize() {
+    let cache_key = 123456;
+    let cache = {
+      let mut cache = HashMap::new();
+      cache.insert(
+        ("specifier1".to_string(), CodeCacheType::EsModule),
+        DenoCompileCodeCacheEntry {
+          source_hash: 1,
+          data: vec![1, 2, 3],
+        },
+      );
+      cache.insert(
+        ("specifier2".to_string(), CodeCacheType::EsModule),
+        DenoCompileCodeCacheEntry {
+          source_hash: 2,
+          data: vec![4, 5, 6],
+        },
+      );
+      cache.insert(
+        ("specifier2".to_string(), CodeCacheType::Script),
+        DenoCompileCodeCacheEntry {
+          source_hash: 2,
+          data: vec![6, 5, 1],
+        },
+      );
+      cache
+    };
+    let mut buffer = Vec::new();
+    serialize_with_writer(&mut BufWriter::new(&mut buffer), cache_key, &cache)
+      .unwrap();
+    let deserialized =
+      deserialize_with_reader(&mut BufReader::new(&buffer[..]), cache_key)
+        .unwrap();
+    assert_eq!(cache, deserialized);
+  }
+
+  #[test]
+  fn serialize_deserialize_empty() {
+    let cache_key = 1234;
+    let cache = HashMap::new();
+    let mut buffer = Vec::new();
+    serialize_with_writer(&mut BufWriter::new(&mut buffer), cache_key, &cache)
+      .unwrap();
+    let deserialized =
+      deserialize_with_reader(&mut BufReader::new(&buffer[..]), cache_key)
+        .unwrap();
+    assert_eq!(cache, deserialized);
+  }
+
+  #[test]
+  fn serialize_deserialize_corrupt() {
+    let buffer = "corrupttestingtestingtesting".as_bytes().to_vec();
+    let err = deserialize_with_reader(&mut BufReader::new(&buffer[..]), 1234)
+      .unwrap_err();
+    assert_eq!(err.to_string(), "Cache key mismatch");
+  }
+
+  #[test]
+  fn code_cache() {
+    let temp_dir = TempDir::new();
+    let file_path = temp_dir.path().join("cache.bin").to_path_buf();
+    let url1 = ModuleSpecifier::parse("https://deno.land/example1.js").unwrap();
+    let url2 = ModuleSpecifier::parse("https://deno.land/example2.js").unwrap();
+    // first run
+    {
+      let code_cache = DenoCompileCodeCache::new(file_path.clone(), 1234);
+      assert!(code_cache
+        .get_sync(&url1, CodeCacheType::EsModule, 0)
+        .is_none());
+      assert!(code_cache
+        .get_sync(&url2, CodeCacheType::EsModule, 1)
+        .is_none());
+      assert!(code_cache.enabled());
+      code_cache.set_sync(url1.clone(), CodeCacheType::EsModule, 0, &[1, 2, 3]);
+      assert!(code_cache.enabled());
+      assert!(!file_path.exists());
+      code_cache.set_sync(url2.clone(), CodeCacheType::EsModule, 1, &[2, 1, 3]);
+      assert!(file_path.exists()); // now the new code cache exists
+      assert!(!code_cache.enabled()); // no longer enabled
+    }
+    // second run
+    {
+      let code_cache = DenoCompileCodeCache::new(file_path.clone(), 1234);
+      assert!(code_cache.enabled());
+      let result1 = code_cache
+        .get_sync(&url1, CodeCacheType::EsModule, 0)
+        .unwrap();
+      assert!(code_cache.enabled());
+      let result2 = code_cache
+        .get_sync(&url2, CodeCacheType::EsModule, 1)
+        .unwrap();
+      assert!(!code_cache.enabled()); // no longer enabled
+      assert_eq!(result1, vec![1, 2, 3]);
+      assert_eq!(result2, vec![2, 1, 3]);
+    }
+
+    // new cache key first run
+    {
+      let code_cache = DenoCompileCodeCache::new(file_path.clone(), 54321);
+      assert!(code_cache
+        .get_sync(&url1, CodeCacheType::EsModule, 0)
+        .is_none());
+      assert!(code_cache
+        .get_sync(&url2, CodeCacheType::EsModule, 1)
+        .is_none());
+      code_cache.set_sync(url1.clone(), CodeCacheType::EsModule, 0, &[2, 2, 3]);
+      code_cache.set_sync(url2.clone(), CodeCacheType::EsModule, 1, &[3, 2, 3]);
+    }
+    // new cache key second run
+    {
+      let code_cache = DenoCompileCodeCache::new(file_path.clone(), 54321);
+      let result1 = code_cache
+        .get_sync(&url1, CodeCacheType::EsModule, 0)
+        .unwrap();
+      assert_eq!(result1, vec![2, 2, 3]);
+      assert!(code_cache
+        .get_sync(&url2, CodeCacheType::EsModule, 5) // different hash will cause none
+        .is_none());
+    }
+  }
+}
diff --git a/cli/standalone/file_system.rs b/cli/standalone/file_system.rs
index 314444630..712c6ee91 100644
--- a/cli/standalone/file_system.rs
+++ b/cli/standalone/file_system.rs
@@ -22,8 +22,8 @@ use super::virtual_fs::FileBackedVfs;
 pub struct DenoCompileFileSystem(Arc<FileBackedVfs>);
 
 impl DenoCompileFileSystem {
-  pub fn new(vfs: FileBackedVfs) -> Self {
-    Self(Arc::new(vfs))
+  pub fn new(vfs: Arc<FileBackedVfs>) -> Self {
+    Self(vfs)
   }
 
   fn error_if_in_vfs(&self, path: &Path) -> FsResult<()> {
diff --git a/cli/standalone/mod.rs b/cli/standalone/mod.rs
index 258de0dad..b9f0b1d5b 100644
--- a/cli/standalone/mod.rs
+++ b/cli/standalone/mod.rs
@@ -5,6 +5,9 @@
 #![allow(dead_code)]
 #![allow(unused_imports)]
 
+use binary::StandaloneData;
+use binary::StandaloneModules;
+use code_cache::DenoCompileCodeCache;
 use deno_ast::MediaType;
 use deno_cache_dir::npm::NpmCacheDir;
 use deno_config::workspace::MappedResolution;
@@ -15,8 +18,10 @@ use deno_core::anyhow::Context;
 use deno_core::error::generic_error;
 use deno_core::error::type_error;
 use deno_core::error::AnyError;
+use deno_core::futures::future::LocalBoxFuture;
 use deno_core::futures::FutureExt;
 use deno_core::v8_set_flags;
+use deno_core::FastString;
 use deno_core::FeatureChecker;
 use deno_core::ModuleLoader;
 use deno_core::ModuleSourceCode;
@@ -24,11 +29,15 @@ use deno_core::ModuleSpecifier;
 use deno_core::ModuleType;
 use deno_core::RequestedModuleType;
 use deno_core::ResolutionKind;
+use deno_core::SourceCodeCacheInfo;
 use deno_npm::npm_rc::ResolvedNpmRc;
 use deno_package_json::PackageJsonDepValue;
+use deno_resolver::npm::NpmReqResolverOptions;
 use deno_runtime::deno_fs;
 use deno_runtime::deno_node::create_host_defined_options;
+use deno_runtime::deno_node::NodeRequireLoader;
 use deno_runtime::deno_node::NodeResolver;
+use deno_runtime::deno_node::PackageJsonResolver;
 use deno_runtime::deno_permissions::Permissions;
 use deno_runtime::deno_permissions::PermissionsContainer;
 use deno_runtime::deno_tls::rustls::RootCertStore;
@@ -38,10 +47,12 @@ use deno_runtime::permissions::RuntimePermissionDescriptorParser;
 use deno_runtime::WorkerExecutionMode;
 use deno_runtime::WorkerLogLevel;
 use deno_semver::npm::NpmPackageReqReference;
-use eszip::EszipRelativeFileBaseUrl;
 use import_map::parse_from_json;
 use node_resolver::analyze::NodeCodeTranslator;
+use node_resolver::errors::ClosestPkgJsonError;
+use node_resolver::NodeModuleKind;
 use node_resolver::NodeResolutionMode;
+use serialization::DenoCompileModuleSource;
 use std::borrow::Cow;
 use std::rc::Rc;
 use std::sync::Arc;
@@ -54,86 +65,102 @@ use crate::args::CacheSetting;
 use crate::args::NpmInstallDepsProvider;
 use crate::args::StorageKeyResolver;
 use crate::cache::Caches;
+use crate::cache::DenoCacheEnvFsAdapter;
 use crate::cache::DenoDirProvider;
+use crate::cache::FastInsecureHasher;
 use crate::cache::NodeAnalysisCache;
 use crate::cache::RealDenoCacheEnv;
 use crate::http_util::HttpClientProvider;
 use crate::node::CliCjsCodeAnalyzer;
+use crate::node::CliNodeCodeTranslator;
 use crate::npm::create_cli_npm_resolver;
+use crate::npm::create_in_npm_pkg_checker;
 use crate::npm::CliByonmNpmResolverCreateOptions;
+use crate::npm::CliManagedInNpmPkgCheckerCreateOptions;
+use crate::npm::CliManagedNpmResolverCreateOptions;
+use crate::npm::CliNpmResolver;
 use crate::npm::CliNpmResolverCreateOptions;
-use crate::npm::CliNpmResolverManagedCreateOptions;
 use crate::npm::CliNpmResolverManagedSnapshotOption;
-use crate::resolver::CjsResolutionStore;
+use crate::npm::CreateInNpmPkgCheckerOptions;
+use crate::resolver::CjsTracker;
 use crate::resolver::CliDenoResolverFs;
-use crate::resolver::CliNodeResolver;
+use crate::resolver::CliNpmReqResolver;
+use crate::resolver::IsCjsResolverOptions;
 use crate::resolver::NpmModuleLoader;
 use crate::util::progress_bar::ProgressBar;
 use crate::util::progress_bar::ProgressBarStyle;
 use crate::util::v8::construct_v8_flags;
+use crate::worker::CliCodeCache;
 use crate::worker::CliMainWorkerFactory;
 use crate::worker::CliMainWorkerOptions;
-use crate::worker::ModuleLoaderAndSourceMapGetter;
+use crate::worker::CreateModuleLoaderResult;
 use crate::worker::ModuleLoaderFactory;
 
 pub mod binary;
+mod code_cache;
 mod file_system;
+mod serialization;
 mod virtual_fs;
 
 pub use binary::extract_standalone;
 pub use binary::is_standalone_binary;
 pub use binary::DenoCompileBinaryWriter;
 
-use self::binary::load_npm_vfs;
 use self::binary::Metadata;
 use self::file_system::DenoCompileFileSystem;
 
-struct WorkspaceEszipModule {
-  specifier: ModuleSpecifier,
-  inner: eszip::Module,
-}
-
-struct WorkspaceEszip {
-  eszip: eszip::EszipV2,
-  root_dir_url: Arc<ModuleSpecifier>,
+struct SharedModuleLoaderState {
+  cjs_tracker: Arc<CjsTracker>,
+  fs: Arc<dyn deno_fs::FileSystem>,
+  modules: StandaloneModules,
+  node_code_translator: Arc<CliNodeCodeTranslator>,
+  node_resolver: Arc<NodeResolver>,
+  npm_module_loader: Arc<NpmModuleLoader>,
+  npm_req_resolver: Arc<CliNpmReqResolver>,
+  npm_resolver: Arc<dyn CliNpmResolver>,
+  workspace_resolver: WorkspaceResolver,
+  code_cache: Option<Arc<dyn CliCodeCache>>,
 }
 
-impl WorkspaceEszip {
-  pub fn get_module(
+impl SharedModuleLoaderState {
+  fn get_code_cache(
     &self,
     specifier: &ModuleSpecifier,
-  ) -> Option<WorkspaceEszipModule> {
-    if specifier.scheme() == "file" {
-      let specifier_key = EszipRelativeFileBaseUrl::new(&self.root_dir_url)
-        .specifier_key(specifier);
-      let module = self.eszip.get_module(&specifier_key)?;
-      let specifier = self.root_dir_url.join(&module.specifier).unwrap();
-      Some(WorkspaceEszipModule {
-        specifier,
-        inner: module,
-      })
-    } else {
-      let module = self.eszip.get_module(specifier.as_str())?;
-      Some(WorkspaceEszipModule {
-        specifier: ModuleSpecifier::parse(&module.specifier).unwrap(),
-        inner: module,
-      })
+    source: &[u8],
+  ) -> Option<SourceCodeCacheInfo> {
+    let Some(code_cache) = &self.code_cache else {
+      return None;
+    };
+    if !code_cache.enabled() {
+      return None;
     }
+    // deno version is already included in the root cache key
+    let hash = FastInsecureHasher::new_without_deno_version()
+      .write_hashable(source)
+      .finish();
+    let data = code_cache.get_sync(
+      specifier,
+      deno_runtime::code_cache::CodeCacheType::EsModule,
+      hash,
+    );
+    Some(SourceCodeCacheInfo {
+      hash,
+      data: data.map(Cow::Owned),
+    })
   }
 }
 
-struct SharedModuleLoaderState {
-  eszip: WorkspaceEszip,
-  workspace_resolver: WorkspaceResolver,
-  node_resolver: Arc<CliNodeResolver>,
-  npm_module_loader: Arc<NpmModuleLoader>,
-}
-
 #[derive(Clone)]
 struct EmbeddedModuleLoader {
   shared: Arc<SharedModuleLoaderState>,
 }
 
+impl std::fmt::Debug for EmbeddedModuleLoader {
+  fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result {
+    f.debug_struct("EmbeddedModuleLoader").finish()
+  }
+}
+
 pub const MODULE_NOT_FOUND: &str = "Module not found";
 pub const UNSUPPORTED_SCHEME: &str = "Unsupported scheme";
 
@@ -158,13 +185,27 @@ impl ModuleLoader for EmbeddedModuleLoader {
         type_error(format!("Referrer uses invalid specifier: {}", err))
       })?
     };
+    let referrer_kind = if self
+      .shared
+      .cjs_tracker
+      .is_maybe_cjs(&referrer, MediaType::from_specifier(&referrer))?
+    {
+      NodeModuleKind::Cjs
+    } else {
+      NodeModuleKind::Esm
+    };
 
     if self.shared.node_resolver.in_npm_package(&referrer) {
       return Ok(
         self
           .shared
           .node_resolver
-          .resolve(raw_specifier, &referrer, NodeResolutionMode::Execution)?
+          .resolve(
+            raw_specifier,
+            &referrer,
+            referrer_kind,
+            NodeResolutionMode::Execution,
+          )?
           .into_url(),
       );
     }
@@ -186,13 +227,13 @@ impl ModuleLoader for EmbeddedModuleLoader {
         self
           .shared
           .node_resolver
-          .resolve_package_sub_path_from_deno_module(
+          .resolve_package_subpath_from_deno_module(
             pkg_json.dir_path(),
             sub_path.as_deref(),
             Some(&referrer),
+            referrer_kind,
             NodeResolutionMode::Execution,
-          )?
-          .into_url(),
+          )?,
       ),
       Ok(MappedResolution::PackageJson {
         dep_result,
@@ -202,14 +243,15 @@ impl ModuleLoader for EmbeddedModuleLoader {
       }) => match dep_result.as_ref().map_err(|e| AnyError::from(e.clone()))? {
         PackageJsonDepValue::Req(req) => self
           .shared
-          .node_resolver
+          .npm_req_resolver
           .resolve_req_with_sub_path(
             req,
             sub_path.as_deref(),
             &referrer,
+            referrer_kind,
             NodeResolutionMode::Execution,
           )
-          .map(|res| res.into_url()),
+          .map_err(AnyError::from),
         PackageJsonDepValue::Workspace(version_req) => {
           let pkg_folder = self
             .shared
@@ -222,13 +264,13 @@ impl ModuleLoader for EmbeddedModuleLoader {
             self
               .shared
               .node_resolver
-              .resolve_package_sub_path_from_deno_module(
+              .resolve_package_subpath_from_deno_module(
                 pkg_folder,
                 sub_path.as_deref(),
                 Some(&referrer),
+                referrer_kind,
                 NodeResolutionMode::Execution,
-              )?
-              .into_url(),
+              )?,
           )
         }
       },
@@ -237,20 +279,19 @@ impl ModuleLoader for EmbeddedModuleLoader {
         if let Ok(reference) =
           NpmPackageReqReference::from_specifier(&specifier)
         {
-          return self
-            .shared
-            .node_resolver
-            .resolve_req_reference(
-              &reference,
-              &referrer,
-              NodeResolutionMode::Execution,
-            )
-            .map(|res| res.into_url());
+          return Ok(self.shared.npm_req_resolver.resolve_req_reference(
+            &reference,
+            &referrer,
+            referrer_kind,
+            NodeResolutionMode::Execution,
+          )?);
         }
 
         if specifier.scheme() == "jsr" {
-          if let Some(module) = self.shared.eszip.get_module(&specifier) {
-            return Ok(module.specifier);
+          if let Some(specifier) =
+            self.shared.modules.resolve_specifier(&specifier)?
+          {
+            return Ok(specifier.clone());
           }
         }
 
@@ -258,16 +299,17 @@ impl ModuleLoader for EmbeddedModuleLoader {
           self
             .shared
             .node_resolver
-            .handle_if_in_node_modules(&specifier)?
+            .handle_if_in_node_modules(&specifier)
             .unwrap_or(specifier),
         )
       }
       Err(err)
         if err.is_unmapped_bare_specifier() && referrer.scheme() == "file" =>
       {
-        let maybe_res = self.shared.node_resolver.resolve_if_for_npm_pkg(
+        let maybe_res = self.shared.npm_req_resolver.resolve_if_for_npm_pkg(
           raw_specifier,
           &referrer,
+          referrer_kind,
           NodeResolutionMode::Execution,
         )?;
         if let Some(res) = maybe_res {
@@ -322,14 +364,19 @@ impl ModuleLoader for EmbeddedModuleLoader {
     }
 
     if self.shared.node_resolver.in_npm_package(original_specifier) {
-      let npm_module_loader = self.shared.npm_module_loader.clone();
+      let shared = self.shared.clone();
       let original_specifier = original_specifier.clone();
       let maybe_referrer = maybe_referrer.cloned();
       return deno_core::ModuleLoadResponse::Async(
         async move {
-          let code_source = npm_module_loader
+          let code_source = shared
+            .npm_module_loader
             .load(&original_specifier, maybe_referrer.as_ref())
             .await?;
+          let code_cache_entry = shared.get_code_cache(
+            &code_source.found_url,
+            code_source.code.as_bytes(),
+          );
           Ok(deno_core::ModuleSource::new_with_redirect(
             match code_source.media_type {
               MediaType::Json => ModuleType::Json,
@@ -338,89 +385,177 @@ impl ModuleLoader for EmbeddedModuleLoader {
             code_source.code,
             &original_specifier,
             &code_source.found_url,
-            None,
+            code_cache_entry,
           ))
         }
         .boxed_local(),
       );
     }
 
-    let Some(module) = self.shared.eszip.get_module(original_specifier) else {
-      return deno_core::ModuleLoadResponse::Sync(Err(type_error(format!(
-        "{MODULE_NOT_FOUND}: {}",
-        original_specifier
-      ))));
-    };
-    let original_specifier = original_specifier.clone();
-
-    deno_core::ModuleLoadResponse::Async(
-      async move {
-        let code = module.inner.source().await.ok_or_else(|| {
-          type_error(format!("Module not found: {}", original_specifier))
-        })?;
-        let code = arc_u8_to_arc_str(code)
-          .map_err(|_| type_error("Module source is not utf-8"))?;
-        Ok(deno_core::ModuleSource::new_with_redirect(
-          match module.inner.kind {
-            eszip::ModuleKind::JavaScript => ModuleType::JavaScript,
-            eszip::ModuleKind::Json => ModuleType::Json,
-            eszip::ModuleKind::Jsonc => {
-              return Err(type_error("jsonc modules not supported"))
-            }
-            eszip::ModuleKind::OpaqueData => {
-              unreachable!();
+    match self.shared.modules.read(original_specifier) {
+      Ok(Some(module)) => {
+        let media_type = module.media_type;
+        let (module_specifier, module_type, module_source) =
+          module.into_parts();
+        let is_maybe_cjs = match self
+          .shared
+          .cjs_tracker
+          .is_maybe_cjs(original_specifier, media_type)
+        {
+          Ok(is_maybe_cjs) => is_maybe_cjs,
+          Err(err) => {
+            return deno_core::ModuleLoadResponse::Sync(Err(type_error(
+              format!("{:?}", err),
+            )));
+          }
+        };
+        if is_maybe_cjs {
+          let original_specifier = original_specifier.clone();
+          let module_specifier = module_specifier.clone();
+          let shared = self.shared.clone();
+          deno_core::ModuleLoadResponse::Async(
+            async move {
+              let source = match module_source {
+                DenoCompileModuleSource::String(string) => {
+                  Cow::Borrowed(string)
+                }
+                DenoCompileModuleSource::Bytes(module_code_bytes) => {
+                  match module_code_bytes {
+                    Cow::Owned(bytes) => Cow::Owned(
+                      crate::util::text_encoding::from_utf8_lossy_owned(bytes),
+                    ),
+                    Cow::Borrowed(bytes) => String::from_utf8_lossy(bytes),
+                  }
+                }
+              };
+              let source = shared
+                .node_code_translator
+                .translate_cjs_to_esm(&module_specifier, Some(source))
+                .await?;
+              let module_source = match source {
+                Cow::Owned(source) => ModuleSourceCode::String(source.into()),
+                Cow::Borrowed(source) => {
+                  ModuleSourceCode::String(FastString::from_static(source))
+                }
+              };
+              let code_cache_entry = shared
+                .get_code_cache(&module_specifier, module_source.as_bytes());
+              Ok(deno_core::ModuleSource::new_with_redirect(
+                module_type,
+                module_source,
+                &original_specifier,
+                &module_specifier,
+                code_cache_entry,
+              ))
             }
-          },
-          ModuleSourceCode::String(code.into()),
-          &original_specifier,
-          &module.specifier,
-          None,
-        ))
+            .boxed_local(),
+          )
+        } else {
+          let module_source = module_source.into_for_v8();
+          let code_cache_entry = self
+            .shared
+            .get_code_cache(module_specifier, module_source.as_bytes());
+          deno_core::ModuleLoadResponse::Sync(Ok(
+            deno_core::ModuleSource::new_with_redirect(
+              module_type,
+              module_source,
+              original_specifier,
+              module_specifier,
+              code_cache_entry,
+            ),
+          ))
+        }
       }
-      .boxed_local(),
-    )
+      Ok(None) => deno_core::ModuleLoadResponse::Sync(Err(type_error(
+        format!("{MODULE_NOT_FOUND}: {}", original_specifier),
+      ))),
+      Err(err) => deno_core::ModuleLoadResponse::Sync(Err(type_error(
+        format!("{:?}", err),
+      ))),
+    }
+  }
+
+  fn code_cache_ready(
+    &self,
+    specifier: ModuleSpecifier,
+    source_hash: u64,
+    code_cache_data: &[u8],
+  ) -> LocalBoxFuture<'static, ()> {
+    if let Some(code_cache) = &self.shared.code_cache {
+      code_cache.set_sync(
+        specifier,
+        deno_runtime::code_cache::CodeCacheType::EsModule,
+        source_hash,
+        code_cache_data,
+      );
+    }
+    std::future::ready(()).boxed_local()
   }
 }
 
-fn arc_u8_to_arc_str(
-  arc_u8: Arc<[u8]>,
-) -> Result<Arc<str>, std::str::Utf8Error> {
-  // Check that the string is valid UTF-8.
-  std::str::from_utf8(&arc_u8)?;
-  // SAFETY: the string is valid UTF-8, and the layout Arc<[u8]> is the same as
-  // Arc<str>. This is proven by the From<Arc<str>> impl for Arc<[u8]> from the
-  // standard library.
-  Ok(unsafe {
-    std::mem::transmute::<std::sync::Arc<[u8]>, std::sync::Arc<str>>(arc_u8)
-  })
+impl NodeRequireLoader for EmbeddedModuleLoader {
+  fn ensure_read_permission<'a>(
+    &self,
+    permissions: &mut dyn deno_runtime::deno_node::NodePermissions,
+    path: &'a std::path::Path,
+  ) -> Result<Cow<'a, std::path::Path>, AnyError> {
+    if self.shared.modules.has_file(path) {
+      // allow reading if the file is in the snapshot
+      return Ok(Cow::Borrowed(path));
+    }
+
+    self
+      .shared
+      .npm_resolver
+      .ensure_read_permission(permissions, path)
+  }
+
+  fn load_text_file_lossy(
+    &self,
+    path: &std::path::Path,
+  ) -> Result<String, AnyError> {
+    Ok(self.shared.fs.read_text_file_lossy_sync(path, None)?)
+  }
+
+  fn is_maybe_cjs(
+    &self,
+    specifier: &ModuleSpecifier,
+  ) -> Result<bool, ClosestPkgJsonError> {
+    let media_type = MediaType::from_specifier(specifier);
+    self.shared.cjs_tracker.is_maybe_cjs(specifier, media_type)
+  }
 }
 
 struct StandaloneModuleLoaderFactory {
   shared: Arc<SharedModuleLoaderState>,
 }
 
+impl StandaloneModuleLoaderFactory {
+  pub fn create_result(&self) -> CreateModuleLoaderResult {
+    let loader = Rc::new(EmbeddedModuleLoader {
+      shared: self.shared.clone(),
+    });
+    CreateModuleLoaderResult {
+      module_loader: loader.clone(),
+      node_require_loader: loader,
+    }
+  }
+}
+
 impl ModuleLoaderFactory for StandaloneModuleLoaderFactory {
   fn create_for_main(
     &self,
     _root_permissions: PermissionsContainer,
-  ) -> ModuleLoaderAndSourceMapGetter {
-    ModuleLoaderAndSourceMapGetter {
-      module_loader: Rc::new(EmbeddedModuleLoader {
-        shared: self.shared.clone(),
-      }),
-    }
+  ) -> CreateModuleLoaderResult {
+    self.create_result()
   }
 
   fn create_for_worker(
     &self,
     _parent_permissions: PermissionsContainer,
     _permissions: PermissionsContainer,
-  ) -> ModuleLoaderAndSourceMapGetter {
-    ModuleLoaderAndSourceMapGetter {
-      module_loader: Rc::new(EmbeddedModuleLoader {
-        shared: self.shared.clone(),
-      }),
-    }
+  ) -> CreateModuleLoaderResult {
+    self.create_result()
   }
 }
 
@@ -439,13 +574,15 @@ impl RootCertStoreProvider for StandaloneRootCertStoreProvider {
   }
 }
 
-pub async fn run(
-  mut eszip: eszip::EszipV2,
-  metadata: Metadata,
-) -> Result<i32, AnyError> {
-  let current_exe_path = std::env::current_exe().unwrap();
-  let current_exe_name =
-    current_exe_path.file_name().unwrap().to_string_lossy();
+pub async fn run(data: StandaloneData) -> Result<i32, AnyError> {
+  let StandaloneData {
+    fs,
+    metadata,
+    modules,
+    npm_snapshot,
+    root_path,
+    vfs,
+  } = data;
   let deno_dir_provider = Arc::new(DenoDirProvider::new(None));
   let root_cert_store_provider = Arc::new(StandaloneRootCertStoreProvider {
     ca_stores: metadata.ca_stores,
@@ -459,44 +596,50 @@ pub async fn run(
   ));
   // use a dummy npm registry url
   let npm_registry_url = ModuleSpecifier::parse("https://localhost/").unwrap();
-  let root_path =
-    std::env::temp_dir().join(format!("deno-compile-{}", current_exe_name));
   let root_dir_url =
     Arc::new(ModuleSpecifier::from_directory_path(&root_path).unwrap());
   let main_module = root_dir_url.join(&metadata.entrypoint_key).unwrap();
-  let root_node_modules_path = root_path.join("node_modules");
-  let npm_cache_dir = NpmCacheDir::new(
-    &RealDenoCacheEnv,
-    root_node_modules_path.clone(),
-    vec![npm_registry_url.clone()],
-  );
-  let npm_global_cache_dir = npm_cache_dir.get_cache_location();
+  let npm_global_cache_dir = root_path.join(".deno_compile_node_modules");
   let cache_setting = CacheSetting::Only;
-  let (fs, npm_resolver, maybe_vfs_root) = match metadata.node_modules {
+  let pkg_json_resolver = Arc::new(PackageJsonResolver::new(
+    deno_runtime::deno_node::DenoFsNodeResolverEnv::new(fs.clone()),
+  ));
+  let (in_npm_pkg_checker, npm_resolver) = match metadata.node_modules {
     Some(binary::NodeModules::Managed { node_modules_dir }) => {
-      // this will always have a snapshot
-      let snapshot = eszip.take_npm_snapshot().unwrap();
-      let vfs_root_dir_path = if node_modules_dir.is_some() {
-        root_path.clone()
-      } else {
-        npm_cache_dir.root_dir().to_owned()
-      };
-      let vfs = load_npm_vfs(vfs_root_dir_path.clone())
-        .context("Failed to load npm vfs.")?;
+      // create an npmrc that uses the fake npm_registry_url to resolve packages
+      let npmrc = Arc::new(ResolvedNpmRc {
+        default_config: deno_npm::npm_rc::RegistryConfigWithUrl {
+          registry_url: npm_registry_url.clone(),
+          config: Default::default(),
+        },
+        scopes: Default::default(),
+        registry_configs: Default::default(),
+      });
+      let npm_cache_dir = Arc::new(NpmCacheDir::new(
+        &DenoCacheEnvFsAdapter(fs.as_ref()),
+        npm_global_cache_dir,
+        npmrc.get_all_known_registries_urls(),
+      ));
+      let snapshot = npm_snapshot.unwrap();
       let maybe_node_modules_path = node_modules_dir
-        .map(|node_modules_dir| vfs_root_dir_path.join(node_modules_dir));
-      let fs = Arc::new(DenoCompileFileSystem::new(vfs))
-        as Arc<dyn deno_fs::FileSystem>;
+        .map(|node_modules_dir| root_path.join(node_modules_dir));
+      let in_npm_pkg_checker =
+        create_in_npm_pkg_checker(CreateInNpmPkgCheckerOptions::Managed(
+          CliManagedInNpmPkgCheckerCreateOptions {
+            root_cache_dir_url: npm_cache_dir.root_dir_url(),
+            maybe_node_modules_path: maybe_node_modules_path.as_deref(),
+          },
+        ));
       let npm_resolver =
         create_cli_npm_resolver(CliNpmResolverCreateOptions::Managed(
-          CliNpmResolverManagedCreateOptions {
+          CliManagedNpmResolverCreateOptions {
             snapshot: CliNpmResolverManagedSnapshotOption::Specified(Some(
               snapshot,
             )),
             maybe_lockfile: None,
             fs: fs.clone(),
             http_client_provider: http_client_provider.clone(),
-            npm_global_cache_dir,
+            npm_cache_dir,
             cache_setting,
             text_only_progress_bar: progress_bar,
             maybe_node_modules_path,
@@ -505,50 +648,54 @@ pub async fn run(
               // this is only used for installing packages, which isn't necessary with deno compile
               NpmInstallDepsProvider::empty(),
             ),
-            // create an npmrc that uses the fake npm_registry_url to resolve packages
-            npmrc: Arc::new(ResolvedNpmRc {
-              default_config: deno_npm::npm_rc::RegistryConfigWithUrl {
-                registry_url: npm_registry_url.clone(),
-                config: Default::default(),
-              },
-              scopes: Default::default(),
-              registry_configs: Default::default(),
-            }),
+            npmrc,
             lifecycle_scripts: Default::default(),
           },
         ))
         .await?;
-      (fs, npm_resolver, Some(vfs_root_dir_path))
+      (in_npm_pkg_checker, npm_resolver)
     }
     Some(binary::NodeModules::Byonm {
       root_node_modules_dir,
     }) => {
-      let vfs_root_dir_path = root_path.clone();
-      let vfs = load_npm_vfs(vfs_root_dir_path.clone())
-        .context("Failed to load vfs.")?;
       let root_node_modules_dir =
         root_node_modules_dir.map(|p| vfs.root().join(p));
-      let fs = Arc::new(DenoCompileFileSystem::new(vfs))
-        as Arc<dyn deno_fs::FileSystem>;
+      let in_npm_pkg_checker =
+        create_in_npm_pkg_checker(CreateInNpmPkgCheckerOptions::Byonm);
       let npm_resolver = create_cli_npm_resolver(
         CliNpmResolverCreateOptions::Byonm(CliByonmNpmResolverCreateOptions {
           fs: CliDenoResolverFs(fs.clone()),
+          pkg_json_resolver: pkg_json_resolver.clone(),
           root_node_modules_dir,
         }),
       )
       .await?;
-      (fs, npm_resolver, Some(vfs_root_dir_path))
+      (in_npm_pkg_checker, npm_resolver)
     }
     None => {
-      let fs = Arc::new(deno_fs::RealFs) as Arc<dyn deno_fs::FileSystem>;
+      // Packages from different registries are already inlined in the binary,
+      // so no need to create actual `.npmrc` configuration.
+      let npmrc = create_default_npmrc();
+      let npm_cache_dir = Arc::new(NpmCacheDir::new(
+        &DenoCacheEnvFsAdapter(fs.as_ref()),
+        npm_global_cache_dir,
+        npmrc.get_all_known_registries_urls(),
+      ));
+      let in_npm_pkg_checker =
+        create_in_npm_pkg_checker(CreateInNpmPkgCheckerOptions::Managed(
+          CliManagedInNpmPkgCheckerCreateOptions {
+            root_cache_dir_url: npm_cache_dir.root_dir_url(),
+            maybe_node_modules_path: None,
+          },
+        ));
       let npm_resolver =
         create_cli_npm_resolver(CliNpmResolverCreateOptions::Managed(
-          CliNpmResolverManagedCreateOptions {
+          CliManagedNpmResolverCreateOptions {
             snapshot: CliNpmResolverManagedSnapshotOption::Specified(None),
             maybe_lockfile: None,
             fs: fs.clone(),
             http_client_provider: http_client_provider.clone(),
-            npm_global_cache_dir,
+            npm_cache_dir,
             cache_setting,
             text_only_progress_bar: progress_bar,
             maybe_node_modules_path: None,
@@ -557,41 +704,53 @@ pub async fn run(
               // this is only used for installing packages, which isn't necessary with deno compile
               NpmInstallDepsProvider::empty(),
             ),
-            // Packages from different registries are already inlined in the ESZip,
-            // so no need to create actual `.npmrc` configuration.
             npmrc: create_default_npmrc(),
             lifecycle_scripts: Default::default(),
           },
         ))
         .await?;
-      (fs, npm_resolver, None)
+      (in_npm_pkg_checker, npm_resolver)
     }
   };
 
   let has_node_modules_dir = npm_resolver.root_node_modules_path().is_some();
   let node_resolver = Arc::new(NodeResolver::new(
     deno_runtime::deno_node::DenoFsNodeResolverEnv::new(fs.clone()),
-    npm_resolver.clone().into_npm_resolver(),
+    in_npm_pkg_checker.clone(),
+    npm_resolver.clone().into_npm_pkg_folder_resolver(),
+    pkg_json_resolver.clone(),
+  ));
+  let cjs_tracker = Arc::new(CjsTracker::new(
+    in_npm_pkg_checker.clone(),
+    pkg_json_resolver.clone(),
+    IsCjsResolverOptions {
+      detect_cjs: !metadata.workspace_resolver.package_jsons.is_empty(),
+      is_node_main: false,
+    },
   ));
-  let cjs_resolutions = Arc::new(CjsResolutionStore::default());
   let cache_db = Caches::new(deno_dir_provider.clone());
   let node_analysis_cache = NodeAnalysisCache::new(cache_db.node_analysis_db());
-  let cli_node_resolver = Arc::new(CliNodeResolver::new(
-    cjs_resolutions.clone(),
-    fs.clone(),
-    node_resolver.clone(),
-    npm_resolver.clone(),
-  ));
+  let npm_req_resolver =
+    Arc::new(CliNpmReqResolver::new(NpmReqResolverOptions {
+      byonm_resolver: (npm_resolver.clone()).into_maybe_byonm(),
+      fs: CliDenoResolverFs(fs.clone()),
+      in_npm_pkg_checker: in_npm_pkg_checker.clone(),
+      node_resolver: node_resolver.clone(),
+      npm_req_resolver: npm_resolver.clone().into_npm_req_resolver(),
+    }));
   let cjs_esm_code_analyzer = CliCjsCodeAnalyzer::new(
     node_analysis_cache,
+    cjs_tracker.clone(),
     fs.clone(),
-    cli_node_resolver.clone(),
+    None,
   );
   let node_code_translator = Arc::new(NodeCodeTranslator::new(
     cjs_esm_code_analyzer,
     deno_runtime::deno_node::DenoFsNodeResolverEnv::new(fs.clone()),
+    in_npm_pkg_checker,
     node_resolver.clone(),
-    npm_resolver.clone().into_npm_resolver(),
+    npm_resolver.clone().into_npm_pkg_folder_resolver(),
+    pkg_json_resolver.clone(),
   ));
   let workspace_resolver = {
     let import_map = match metadata.workspace_resolver.import_map {
@@ -642,39 +801,52 @@ pub async fn run(
       metadata.workspace_resolver.pkg_json_resolution,
     )
   };
+  let code_cache = match metadata.code_cache_key {
+    Some(code_cache_key) => Some(Arc::new(DenoCompileCodeCache::new(
+      root_path.with_file_name(format!(
+        "{}.cache",
+        root_path.file_name().unwrap().to_string_lossy()
+      )),
+      code_cache_key,
+    )) as Arc<dyn CliCodeCache>),
+    None => {
+      log::debug!("Code cache disabled.");
+      None
+    }
+  };
   let module_loader_factory = StandaloneModuleLoaderFactory {
     shared: Arc::new(SharedModuleLoaderState {
-      eszip: WorkspaceEszip {
-        eszip,
-        root_dir_url,
-      },
-      workspace_resolver,
-      node_resolver: cli_node_resolver.clone(),
+      cjs_tracker: cjs_tracker.clone(),
+      fs: fs.clone(),
+      modules,
+      node_code_translator: node_code_translator.clone(),
+      node_resolver: node_resolver.clone(),
       npm_module_loader: Arc::new(NpmModuleLoader::new(
-        cjs_resolutions,
-        node_code_translator,
+        cjs_tracker.clone(),
         fs.clone(),
-        cli_node_resolver,
+        node_code_translator,
       )),
+      code_cache: code_cache.clone(),
+      npm_resolver: npm_resolver.clone(),
+      workspace_resolver,
+      npm_req_resolver,
     }),
   };
 
   let permissions = {
     let mut permissions =
       metadata.permissions.to_options(/* cli_arg_urls */ &[]);
-    // if running with an npm vfs, grant read access to it
-    if let Some(vfs_root) = maybe_vfs_root {
-      match &mut permissions.allow_read {
-        Some(vec) if vec.is_empty() => {
-          // do nothing, already granted
-        }
-        Some(vec) => {
-          vec.push(vfs_root.to_string_lossy().to_string());
-        }
-        None => {
-          permissions.allow_read =
-            Some(vec![vfs_root.to_string_lossy().to_string()]);
-        }
+    // grant read access to the vfs
+    match &mut permissions.allow_read {
+      Some(vec) if vec.is_empty() => {
+        // do nothing, already granted
+      }
+      Some(vec) => {
+        vec.push(root_path.to_string_lossy().to_string());
+      }
+      None => {
+        permissions.allow_read =
+          Some(vec![root_path.to_string_lossy().to_string()]);
       }
     }
 
@@ -696,8 +868,7 @@ pub async fn run(
   });
   let worker_factory = CliMainWorkerFactory::new(
     Arc::new(BlobStore::default()),
-    // Code cache is not supported for standalone binary yet.
-    None,
+    code_cache,
     feature_checker,
     fs,
     None,
@@ -706,6 +877,7 @@ pub async fn run(
     Box::new(module_loader_factory),
     node_resolver,
     npm_resolver,
+    pkg_json_resolver,
     root_cert_store_provider,
     permissions,
     StorageKeyResolver::empty(),
@@ -721,7 +893,6 @@ pub async fn run(
       inspect_wait: false,
       strace_ops: None,
       is_inspecting: false,
-      is_npm_main: main_module.scheme() == "npm",
       skip_op_registration: true,
       location: metadata.location,
       argv0: NpmPackageReqReference::from_specifier(&main_module)
@@ -739,6 +910,7 @@ pub async fn run(
       serve_port: None,
       serve_host: None,
     },
+    metadata.otel_config,
   );
 
   // Initialize v8 once from the main thread.
diff --git a/cli/standalone/serialization.rs b/cli/standalone/serialization.rs
new file mode 100644
index 000000000..a5eb649bf
--- /dev/null
+++ b/cli/standalone/serialization.rs
@@ -0,0 +1,661 @@
+// Copyright 2018-2024 the Deno authors. All rights reserved. MIT license.
+
+use std::borrow::Cow;
+use std::collections::BTreeMap;
+use std::collections::HashMap;
+use std::io::Write;
+
+use deno_ast::MediaType;
+use deno_core::anyhow::bail;
+use deno_core::anyhow::Context;
+use deno_core::error::AnyError;
+use deno_core::serde_json;
+use deno_core::url::Url;
+use deno_core::FastString;
+use deno_core::ModuleSourceCode;
+use deno_core::ModuleType;
+use deno_npm::resolution::SerializedNpmResolutionSnapshot;
+use deno_npm::resolution::SerializedNpmResolutionSnapshotPackage;
+use deno_npm::resolution::ValidSerializedNpmResolutionSnapshot;
+use deno_npm::NpmPackageId;
+use deno_semver::package::PackageReq;
+
+use crate::standalone::virtual_fs::VirtualDirectory;
+
+use super::binary::Metadata;
+use super::virtual_fs::VfsBuilder;
+
+const MAGIC_BYTES: &[u8; 8] = b"d3n0l4nd";
+
+/// Binary format:
+/// * d3n0l4nd
+/// * <metadata_len><metadata>
+/// * <npm_snapshot_len><npm_snapshot>
+/// * <remote_modules_len><remote_modules>
+/// * <vfs_headers_len><vfs_headers>
+/// * <vfs_file_data_len><vfs_file_data>
+/// * d3n0l4nd
+pub fn serialize_binary_data_section(
+  metadata: &Metadata,
+  npm_snapshot: Option<SerializedNpmResolutionSnapshot>,
+  remote_modules: &RemoteModulesStoreBuilder,
+  vfs: VfsBuilder,
+) -> Result<Vec<u8>, AnyError> {
+  fn write_bytes_with_len(bytes: &mut Vec<u8>, data: &[u8]) {
+    bytes.extend_from_slice(&(data.len() as u64).to_le_bytes());
+    bytes.extend_from_slice(data);
+  }
+
+  let mut bytes = Vec::new();
+  bytes.extend_from_slice(MAGIC_BYTES);
+
+  // 1. Metadata
+  {
+    let metadata = serde_json::to_string(metadata)?;
+    write_bytes_with_len(&mut bytes, metadata.as_bytes());
+  }
+  // 2. Npm snapshot
+  {
+    let npm_snapshot =
+      npm_snapshot.map(serialize_npm_snapshot).unwrap_or_default();
+    write_bytes_with_len(&mut bytes, &npm_snapshot);
+  }
+  // 3. Remote modules
+  {
+    let update_index = bytes.len();
+    bytes.extend_from_slice(&(0_u64).to_le_bytes());
+    let start_index = bytes.len();
+    remote_modules.write(&mut bytes)?;
+    let length = bytes.len() - start_index;
+    let length_bytes = (length as u64).to_le_bytes();
+    bytes[update_index..update_index + length_bytes.len()]
+      .copy_from_slice(&length_bytes);
+  }
+  // 4. VFS
+  {
+    let (vfs, vfs_files) = vfs.into_dir_and_files();
+    let vfs = serde_json::to_string(&vfs)?;
+    write_bytes_with_len(&mut bytes, vfs.as_bytes());
+    let vfs_bytes_len = vfs_files.iter().map(|f| f.len() as u64).sum::<u64>();
+    bytes.extend_from_slice(&vfs_bytes_len.to_le_bytes());
+    for file in &vfs_files {
+      bytes.extend_from_slice(file);
+    }
+  }
+
+  // write the magic bytes at the end so we can use it
+  // to make sure we've deserialized correctly
+  bytes.extend_from_slice(MAGIC_BYTES);
+
+  Ok(bytes)
+}
+
+pub struct DeserializedDataSection {
+  pub metadata: Metadata,
+  pub npm_snapshot: Option<ValidSerializedNpmResolutionSnapshot>,
+  pub remote_modules: RemoteModulesStore,
+  pub vfs_dir: VirtualDirectory,
+  pub vfs_files_data: &'static [u8],
+}
+
+pub fn deserialize_binary_data_section(
+  data: &'static [u8],
+) -> Result<Option<DeserializedDataSection>, AnyError> {
+  fn read_bytes_with_len(input: &[u8]) -> Result<(&[u8], &[u8]), AnyError> {
+    let (input, len) = read_u64(input)?;
+    let (input, data) = read_bytes(input, len as usize)?;
+    Ok((input, data))
+  }
+
+  fn read_magic_bytes(input: &[u8]) -> Result<(&[u8], bool), AnyError> {
+    if input.len() < MAGIC_BYTES.len() {
+      bail!("Unexpected end of data. Could not find magic bytes.");
+    }
+    let (magic_bytes, input) = input.split_at(MAGIC_BYTES.len());
+    if magic_bytes != MAGIC_BYTES {
+      return Ok((input, false));
+    }
+    Ok((input, true))
+  }
+
+  let (input, found) = read_magic_bytes(data)?;
+  if !found {
+    return Ok(None);
+  }
+
+  // 1. Metadata
+  let (input, data) = read_bytes_with_len(input).context("reading metadata")?;
+  let metadata: Metadata =
+    serde_json::from_slice(data).context("deserializing metadata")?;
+  // 2. Npm snapshot
+  let (input, data) =
+    read_bytes_with_len(input).context("reading npm snapshot")?;
+  let npm_snapshot = if data.is_empty() {
+    None
+  } else {
+    Some(deserialize_npm_snapshot(data).context("deserializing npm snapshot")?)
+  };
+  // 3. Remote modules
+  let (input, data) =
+    read_bytes_with_len(input).context("reading remote modules data")?;
+  let remote_modules =
+    RemoteModulesStore::build(data).context("deserializing remote modules")?;
+  // 4. VFS
+  let (input, data) = read_bytes_with_len(input).context("vfs")?;
+  let vfs_dir: VirtualDirectory =
+    serde_json::from_slice(data).context("deserializing vfs data")?;
+  let (input, vfs_files_data) =
+    read_bytes_with_len(input).context("reading vfs files data")?;
+
+  // finally ensure we read the magic bytes at the end
+  let (_input, found) = read_magic_bytes(input)?;
+  if !found {
+    bail!("Could not find magic bytes at the end of the data.");
+  }
+
+  Ok(Some(DeserializedDataSection {
+    metadata,
+    npm_snapshot,
+    remote_modules,
+    vfs_dir,
+    vfs_files_data,
+  }))
+}
+
+#[derive(Default)]
+pub struct RemoteModulesStoreBuilder {
+  specifiers: Vec<(String, u64)>,
+  data: Vec<(MediaType, Vec<u8>)>,
+  data_byte_len: u64,
+  redirects: Vec<(String, String)>,
+  redirects_len: u64,
+}
+
+impl RemoteModulesStoreBuilder {
+  pub fn add(&mut self, specifier: &Url, media_type: MediaType, data: Vec<u8>) {
+    log::debug!("Adding '{}' ({})", specifier, media_type);
+    let specifier = specifier.to_string();
+    self.specifiers.push((specifier, self.data_byte_len));
+    self.data_byte_len += 1 + 8 + data.len() as u64; // media type (1 byte), data length (8 bytes), data
+    self.data.push((media_type, data));
+  }
+
+  pub fn add_redirects(&mut self, redirects: &BTreeMap<Url, Url>) {
+    self.redirects.reserve(redirects.len());
+    for (from, to) in redirects {
+      log::debug!("Adding redirect '{}' -> '{}'", from, to);
+      let from = from.to_string();
+      let to = to.to_string();
+      self.redirects_len += (4 + from.len() + 4 + to.len()) as u64;
+      self.redirects.push((from, to));
+    }
+  }
+
+  fn write(&self, writer: &mut dyn Write) -> Result<(), AnyError> {
+    writer.write_all(&(self.specifiers.len() as u32).to_le_bytes())?;
+    writer.write_all(&(self.redirects.len() as u32).to_le_bytes())?;
+    for (specifier, offset) in &self.specifiers {
+      writer.write_all(&(specifier.len() as u32).to_le_bytes())?;
+      writer.write_all(specifier.as_bytes())?;
+      writer.write_all(&offset.to_le_bytes())?;
+    }
+    for (from, to) in &self.redirects {
+      writer.write_all(&(from.len() as u32).to_le_bytes())?;
+      writer.write_all(from.as_bytes())?;
+      writer.write_all(&(to.len() as u32).to_le_bytes())?;
+      writer.write_all(to.as_bytes())?;
+    }
+    for (media_type, data) in &self.data {
+      writer.write_all(&[serialize_media_type(*media_type)])?;
+      writer.write_all(&(data.len() as u64).to_le_bytes())?;
+      writer.write_all(data)?;
+    }
+    Ok(())
+  }
+}
+
+pub enum DenoCompileModuleSource {
+  String(&'static str),
+  Bytes(Cow<'static, [u8]>),
+}
+
+impl DenoCompileModuleSource {
+  pub fn into_for_v8(self) -> ModuleSourceCode {
+    fn into_bytes(data: Cow<'static, [u8]>) -> ModuleSourceCode {
+      ModuleSourceCode::Bytes(match data {
+        Cow::Borrowed(d) => d.into(),
+        Cow::Owned(d) => d.into_boxed_slice().into(),
+      })
+    }
+
+    match self {
+      // todo(https://github.com/denoland/deno_core/pull/943): store whether
+      // the string is ascii or not ahead of time so we can avoid the is_ascii()
+      // check in FastString::from_static
+      Self::String(s) => ModuleSourceCode::String(FastString::from_static(s)),
+      Self::Bytes(b) => into_bytes(b),
+    }
+  }
+}
+
+pub struct DenoCompileModuleData<'a> {
+  pub specifier: &'a Url,
+  pub media_type: MediaType,
+  pub data: Cow<'static, [u8]>,
+}
+
+impl<'a> DenoCompileModuleData<'a> {
+  pub fn into_parts(self) -> (&'a Url, ModuleType, DenoCompileModuleSource) {
+    fn into_string_unsafe(data: Cow<'static, [u8]>) -> DenoCompileModuleSource {
+      match data {
+        Cow::Borrowed(d) => DenoCompileModuleSource::String(
+          // SAFETY: we know this is a valid utf8 string
+          unsafe { std::str::from_utf8_unchecked(d) },
+        ),
+        Cow::Owned(d) => DenoCompileModuleSource::Bytes(Cow::Owned(d)),
+      }
+    }
+
+    let (media_type, source) = match self.media_type {
+      MediaType::JavaScript
+      | MediaType::Jsx
+      | MediaType::Mjs
+      | MediaType::Cjs
+      | MediaType::TypeScript
+      | MediaType::Mts
+      | MediaType::Cts
+      | MediaType::Dts
+      | MediaType::Dmts
+      | MediaType::Dcts
+      | MediaType::Tsx => {
+        (ModuleType::JavaScript, into_string_unsafe(self.data))
+      }
+      MediaType::Json => (ModuleType::Json, into_string_unsafe(self.data)),
+      MediaType::Wasm => {
+        (ModuleType::Wasm, DenoCompileModuleSource::Bytes(self.data))
+      }
+      // just assume javascript if we made it here
+      MediaType::Css | MediaType::SourceMap | MediaType::Unknown => (
+        ModuleType::JavaScript,
+        DenoCompileModuleSource::Bytes(self.data),
+      ),
+    };
+    (self.specifier, media_type, source)
+  }
+}
+
+enum RemoteModulesStoreSpecifierValue {
+  Data(usize),
+  Redirect(Url),
+}
+
+pub struct RemoteModulesStore {
+  specifiers: HashMap<Url, RemoteModulesStoreSpecifierValue>,
+  files_data: &'static [u8],
+}
+
+impl RemoteModulesStore {
+  fn build(data: &'static [u8]) -> Result<Self, AnyError> {
+    fn read_specifier(input: &[u8]) -> Result<(&[u8], (Url, u64)), AnyError> {
+      let (input, specifier) = read_string_lossy(input)?;
+      let specifier = Url::parse(&specifier)?;
+      let (input, offset) = read_u64(input)?;
+      Ok((input, (specifier, offset)))
+    }
+
+    fn read_redirect(input: &[u8]) -> Result<(&[u8], (Url, Url)), AnyError> {
+      let (input, from) = read_string_lossy(input)?;
+      let from = Url::parse(&from)?;
+      let (input, to) = read_string_lossy(input)?;
+      let to = Url::parse(&to)?;
+      Ok((input, (from, to)))
+    }
+
+    fn read_headers(
+      input: &[u8],
+    ) -> Result<(&[u8], HashMap<Url, RemoteModulesStoreSpecifierValue>), AnyError>
+    {
+      let (input, specifiers_len) = read_u32_as_usize(input)?;
+      let (mut input, redirects_len) = read_u32_as_usize(input)?;
+      let mut specifiers =
+        HashMap::with_capacity(specifiers_len + redirects_len);
+      for _ in 0..specifiers_len {
+        let (current_input, (specifier, offset)) =
+          read_specifier(input).context("reading specifier")?;
+        input = current_input;
+        specifiers.insert(
+          specifier,
+          RemoteModulesStoreSpecifierValue::Data(offset as usize),
+        );
+      }
+
+      for _ in 0..redirects_len {
+        let (current_input, (from, to)) = read_redirect(input)?;
+        input = current_input;
+        specifiers.insert(from, RemoteModulesStoreSpecifierValue::Redirect(to));
+      }
+
+      Ok((input, specifiers))
+    }
+
+    let (files_data, specifiers) = read_headers(data)?;
+
+    Ok(Self {
+      specifiers,
+      files_data,
+    })
+  }
+
+  pub fn resolve_specifier<'a>(
+    &'a self,
+    specifier: &'a Url,
+  ) -> Result<Option<&'a Url>, AnyError> {
+    let mut count = 0;
+    let mut current = specifier;
+    loop {
+      if count > 10 {
+        bail!("Too many redirects resolving '{}'", specifier);
+      }
+      match self.specifiers.get(current) {
+        Some(RemoteModulesStoreSpecifierValue::Redirect(to)) => {
+          current = to;
+          count += 1;
+        }
+        Some(RemoteModulesStoreSpecifierValue::Data(_)) => {
+          return Ok(Some(current));
+        }
+        None => {
+          return Ok(None);
+        }
+      }
+    }
+  }
+
+  pub fn read<'a>(
+    &'a self,
+    original_specifier: &'a Url,
+  ) -> Result<Option<DenoCompileModuleData<'a>>, AnyError> {
+    let mut count = 0;
+    let mut specifier = original_specifier;
+    loop {
+      if count > 10 {
+        bail!("Too many redirects resolving '{}'", original_specifier);
+      }
+      match self.specifiers.get(specifier) {
+        Some(RemoteModulesStoreSpecifierValue::Redirect(to)) => {
+          specifier = to;
+          count += 1;
+        }
+        Some(RemoteModulesStoreSpecifierValue::Data(offset)) => {
+          let input = &self.files_data[*offset..];
+          let (input, media_type_byte) = read_bytes(input, 1)?;
+          let media_type = deserialize_media_type(media_type_byte[0])?;
+          let (input, len) = read_u64(input)?;
+          let (_input, data) = read_bytes(input, len as usize)?;
+          return Ok(Some(DenoCompileModuleData {
+            specifier,
+            media_type,
+            data: Cow::Borrowed(data),
+          }));
+        }
+        None => {
+          return Ok(None);
+        }
+      }
+    }
+  }
+}
+
+fn serialize_npm_snapshot(
+  mut snapshot: SerializedNpmResolutionSnapshot,
+) -> Vec<u8> {
+  fn append_string(bytes: &mut Vec<u8>, string: &str) {
+    let len = string.len() as u32;
+    bytes.extend_from_slice(&len.to_le_bytes());
+    bytes.extend_from_slice(string.as_bytes());
+  }
+
+  snapshot.packages.sort_by(|a, b| a.id.cmp(&b.id)); // determinism
+  let ids_to_stored_ids = snapshot
+    .packages
+    .iter()
+    .enumerate()
+    .map(|(i, pkg)| (&pkg.id, i as u32))
+    .collect::<HashMap<_, _>>();
+
+  let mut root_packages: Vec<_> = snapshot.root_packages.iter().collect();
+  root_packages.sort();
+  let mut bytes = Vec::new();
+
+  bytes.extend_from_slice(&(snapshot.packages.len() as u32).to_le_bytes());
+  for pkg in &snapshot.packages {
+    append_string(&mut bytes, &pkg.id.as_serialized());
+  }
+
+  bytes.extend_from_slice(&(root_packages.len() as u32).to_le_bytes());
+  for (req, id) in root_packages {
+    append_string(&mut bytes, &req.to_string());
+    let id = ids_to_stored_ids.get(&id).unwrap();
+    bytes.extend_from_slice(&id.to_le_bytes());
+  }
+
+  for pkg in &snapshot.packages {
+    let deps_len = pkg.dependencies.len() as u32;
+    bytes.extend_from_slice(&deps_len.to_le_bytes());
+    let mut deps: Vec<_> = pkg.dependencies.iter().collect();
+    deps.sort();
+    for (req, id) in deps {
+      append_string(&mut bytes, req);
+      let id = ids_to_stored_ids.get(&id).unwrap();
+      bytes.extend_from_slice(&id.to_le_bytes());
+    }
+  }
+
+  bytes
+}
+
+fn deserialize_npm_snapshot(
+  input: &[u8],
+) -> Result<ValidSerializedNpmResolutionSnapshot, AnyError> {
+  fn parse_id(input: &[u8]) -> Result<(&[u8], NpmPackageId), AnyError> {
+    let (input, id) = read_string_lossy(input)?;
+    let id = NpmPackageId::from_serialized(&id)?;
+    Ok((input, id))
+  }
+
+  #[allow(clippy::needless_lifetimes)] // clippy bug
+  fn parse_root_package<'a>(
+    id_to_npm_id: &'a impl Fn(usize) -> Result<NpmPackageId, AnyError>,
+  ) -> impl Fn(&[u8]) -> Result<(&[u8], (PackageReq, NpmPackageId)), AnyError> + 'a
+  {
+    |input| {
+      let (input, req) = read_string_lossy(input)?;
+      let req = PackageReq::from_str(&req)?;
+      let (input, id) = read_u32_as_usize(input)?;
+      Ok((input, (req, id_to_npm_id(id)?)))
+    }
+  }
+
+  #[allow(clippy::needless_lifetimes)] // clippy bug
+  fn parse_package_dep<'a>(
+    id_to_npm_id: &'a impl Fn(usize) -> Result<NpmPackageId, AnyError>,
+  ) -> impl Fn(&[u8]) -> Result<(&[u8], (String, NpmPackageId)), AnyError> + 'a
+  {
+    |input| {
+      let (input, req) = read_string_lossy(input)?;
+      let (input, id) = read_u32_as_usize(input)?;
+      Ok((input, (req.into_owned(), id_to_npm_id(id)?)))
+    }
+  }
+
+  fn parse_package<'a>(
+    input: &'a [u8],
+    id: NpmPackageId,
+    id_to_npm_id: &impl Fn(usize) -> Result<NpmPackageId, AnyError>,
+  ) -> Result<(&'a [u8], SerializedNpmResolutionSnapshotPackage), AnyError> {
+    let (input, deps_len) = read_u32_as_usize(input)?;
+    let (input, dependencies) =
+      parse_hashmap_n_times(input, deps_len, parse_package_dep(id_to_npm_id))?;
+    Ok((
+      input,
+      SerializedNpmResolutionSnapshotPackage {
+        id,
+        system: Default::default(),
+        dist: Default::default(),
+        dependencies,
+        optional_dependencies: Default::default(),
+        bin: None,
+        scripts: Default::default(),
+        deprecated: Default::default(),
+      },
+    ))
+  }
+
+  let (input, packages_len) = read_u32_as_usize(input)?;
+
+  // get a hashmap of all the npm package ids to their serialized ids
+  let (input, data_ids_to_npm_ids) =
+    parse_vec_n_times(input, packages_len, parse_id)
+      .context("deserializing id")?;
+  let data_id_to_npm_id = |id: usize| {
+    data_ids_to_npm_ids
+      .get(id)
+      .cloned()
+      .ok_or_else(|| deno_core::anyhow::anyhow!("Invalid npm package id"))
+  };
+
+  let (input, root_packages_len) = read_u32_as_usize(input)?;
+  let (input, root_packages) = parse_hashmap_n_times(
+    input,
+    root_packages_len,
+    parse_root_package(&data_id_to_npm_id),
+  )
+  .context("deserializing root package")?;
+  let (input, packages) =
+    parse_vec_n_times_with_index(input, packages_len, |input, index| {
+      parse_package(input, data_id_to_npm_id(index)?, &data_id_to_npm_id)
+    })
+    .context("deserializing package")?;
+
+  if !input.is_empty() {
+    bail!("Unexpected data left over");
+  }
+
+  Ok(
+    SerializedNpmResolutionSnapshot {
+      packages,
+      root_packages,
+    }
+    // this is ok because we have already verified that all the
+    // identifiers found in the snapshot are valid via the
+    // npm package id -> npm package id mapping
+    .into_valid_unsafe(),
+  )
+}
+
+fn serialize_media_type(media_type: MediaType) -> u8 {
+  match media_type {
+    MediaType::JavaScript => 0,
+    MediaType::Jsx => 1,
+    MediaType::Mjs => 2,
+    MediaType::Cjs => 3,
+    MediaType::TypeScript => 4,
+    MediaType::Mts => 5,
+    MediaType::Cts => 6,
+    MediaType::Dts => 7,
+    MediaType::Dmts => 8,
+    MediaType::Dcts => 9,
+    MediaType::Tsx => 10,
+    MediaType::Json => 11,
+    MediaType::Wasm => 12,
+    MediaType::Css => 13,
+    MediaType::SourceMap => 14,
+    MediaType::Unknown => 15,
+  }
+}
+
+fn deserialize_media_type(value: u8) -> Result<MediaType, AnyError> {
+  match value {
+    0 => Ok(MediaType::JavaScript),
+    1 => Ok(MediaType::Jsx),
+    2 => Ok(MediaType::Mjs),
+    3 => Ok(MediaType::Cjs),
+    4 => Ok(MediaType::TypeScript),
+    5 => Ok(MediaType::Mts),
+    6 => Ok(MediaType::Cts),
+    7 => Ok(MediaType::Dts),
+    8 => Ok(MediaType::Dmts),
+    9 => Ok(MediaType::Dcts),
+    10 => Ok(MediaType::Tsx),
+    11 => Ok(MediaType::Json),
+    12 => Ok(MediaType::Wasm),
+    13 => Ok(MediaType::Css),
+    14 => Ok(MediaType::SourceMap),
+    15 => Ok(MediaType::Unknown),
+    _ => bail!("Unknown media type value: {}", value),
+  }
+}
+
+fn parse_hashmap_n_times<TKey: std::cmp::Eq + std::hash::Hash, TValue>(
+  mut input: &[u8],
+  times: usize,
+  parse: impl Fn(&[u8]) -> Result<(&[u8], (TKey, TValue)), AnyError>,
+) -> Result<(&[u8], HashMap<TKey, TValue>), AnyError> {
+  let mut results = HashMap::with_capacity(times);
+  for _ in 0..times {
+    let result = parse(input);
+    let (new_input, (key, value)) = result?;
+    results.insert(key, value);
+    input = new_input;
+  }
+  Ok((input, results))
+}
+
+fn parse_vec_n_times<TResult>(
+  input: &[u8],
+  times: usize,
+  parse: impl Fn(&[u8]) -> Result<(&[u8], TResult), AnyError>,
+) -> Result<(&[u8], Vec<TResult>), AnyError> {
+  parse_vec_n_times_with_index(input, times, |input, _index| parse(input))
+}
+
+fn parse_vec_n_times_with_index<TResult>(
+  mut input: &[u8],
+  times: usize,
+  parse: impl Fn(&[u8], usize) -> Result<(&[u8], TResult), AnyError>,
+) -> Result<(&[u8], Vec<TResult>), AnyError> {
+  let mut results = Vec::with_capacity(times);
+  for i in 0..times {
+    let result = parse(input, i);
+    let (new_input, result) = result?;
+    results.push(result);
+    input = new_input;
+  }
+  Ok((input, results))
+}
+
+fn read_bytes(input: &[u8], len: usize) -> Result<(&[u8], &[u8]), AnyError> {
+  if input.len() < len {
+    bail!("Unexpected end of data.",);
+  }
+  let (len_bytes, input) = input.split_at(len);
+  Ok((input, len_bytes))
+}
+
+fn read_string_lossy(input: &[u8]) -> Result<(&[u8], Cow<str>), AnyError> {
+  let (input, str_len) = read_u32_as_usize(input)?;
+  let (input, data_bytes) = read_bytes(input, str_len)?;
+  Ok((input, String::from_utf8_lossy(data_bytes)))
+}
+
+fn read_u32_as_usize(input: &[u8]) -> Result<(&[u8], usize), AnyError> {
+  let (input, len_bytes) = read_bytes(input, 4)?;
+  let len = u32::from_le_bytes(len_bytes.try_into()?);
+  Ok((input, len as usize))
+}
+
+fn read_u64(input: &[u8]) -> Result<(&[u8], u64), AnyError> {
+  let (input, len_bytes) = read_bytes(input, 8)?;
+  let len = u64::from_le_bytes(len_bytes.try_into()?);
+  Ok((input, len))
+}
diff --git a/cli/standalone/virtual_fs.rs b/cli/standalone/virtual_fs.rs
index 53d045b62..26bb0db75 100644
--- a/cli/standalone/virtual_fs.rs
+++ b/cli/standalone/virtual_fs.rs
@@ -7,6 +7,7 @@ use std::fs::File;
 use std::io::Read;
 use std::io::Seek;
 use std::io::SeekFrom;
+use std::ops::Range;
 use std::path::Path;
 use std::path::PathBuf;
 use std::rc::Rc;
@@ -67,6 +68,26 @@ impl VfsBuilder {
     })
   }
 
+  pub fn set_new_root_path(
+    &mut self,
+    root_path: PathBuf,
+  ) -> Result<(), AnyError> {
+    let root_path = canonicalize_path(&root_path)?;
+    self.root_path = root_path;
+    self.root_dir = VirtualDirectory {
+      name: self
+        .root_path
+        .file_stem()
+        .map(|s| s.to_string_lossy().into_owned())
+        .unwrap_or("root".to_string()),
+      entries: vec![VfsEntry::Dir(VirtualDirectory {
+        name: std::mem::take(&mut self.root_dir.name),
+        entries: std::mem::take(&mut self.root_dir.entries),
+      })],
+    };
+    Ok(())
+  }
+
   pub fn with_root_dir<R>(
     &mut self,
     with_root: impl FnOnce(&mut VirtualDirectory) -> R,
@@ -119,7 +140,7 @@ impl VfsBuilder {
                 // inline the symlink and make the target file
                 let file_bytes = std::fs::read(&target)
                   .with_context(|| format!("Reading {}", path.display()))?;
-                self.add_file(&path, file_bytes)?;
+                self.add_file_with_data_inner(&path, file_bytes)?;
               } else {
                 log::warn!(
                   "{} Symlink target is outside '{}'. Excluding symlink at '{}' with target '{}'.",
@@ -191,16 +212,32 @@ impl VfsBuilder {
     self.add_file_at_path_not_symlink(&target_path)
   }
 
-  pub fn add_file_at_path_not_symlink(
+  fn add_file_at_path_not_symlink(
     &mut self,
     path: &Path,
   ) -> Result<(), AnyError> {
     let file_bytes = std::fs::read(path)
       .with_context(|| format!("Reading {}", path.display()))?;
-    self.add_file(path, file_bytes)
+    self.add_file_with_data_inner(path, file_bytes)
   }
 
-  fn add_file(&mut self, path: &Path, data: Vec<u8>) -> Result<(), AnyError> {
+  pub fn add_file_with_data(
+    &mut self,
+    path: &Path,
+    data: Vec<u8>,
+  ) -> Result<(), AnyError> {
+    let target_path = canonicalize_path(path)?;
+    if target_path != path {
+      self.add_symlink(path, &target_path)?;
+    }
+    self.add_file_with_data_inner(&target_path, data)
+  }
+
+  fn add_file_with_data_inner(
+    &mut self,
+    path: &Path,
+    data: Vec<u8>,
+  ) -> Result<(), AnyError> {
     log::debug!("Adding file '{}'", path.display());
     let checksum = util::checksum::gen(&[&data]);
     let offset = if let Some(offset) = self.file_offsets.get(&checksum) {
@@ -249,8 +286,15 @@ impl VfsBuilder {
       path.display(),
       target.display()
     );
-    let dest = self.path_relative_root(target)?;
-    if dest == self.path_relative_root(path)? {
+    let relative_target = self.path_relative_root(target)?;
+    let relative_path = match self.path_relative_root(path) {
+      Ok(path) => path,
+      Err(StripRootError { .. }) => {
+        // ignore if the original path is outside the root directory
+        return Ok(());
+      }
+    };
+    if relative_target == relative_path {
       // it's the same, ignore
       return Ok(());
     }
@@ -263,7 +307,7 @@ impl VfsBuilder {
           insert_index,
           VfsEntry::Symlink(VirtualSymlink {
             name: name.to_string(),
-            dest_parts: dest
+            dest_parts: relative_target
               .components()
               .map(|c| c.as_os_str().to_string_lossy().to_string())
               .collect::<Vec<_>>(),
@@ -306,6 +350,7 @@ impl<'a> VfsEntryRef<'a> {
         atime: None,
         birthtime: None,
         mtime: None,
+        ctime: None,
         blksize: 0,
         size: 0,
         dev: 0,
@@ -328,6 +373,7 @@ impl<'a> VfsEntryRef<'a> {
         atime: None,
         birthtime: None,
         mtime: None,
+        ctime: None,
         blksize: 0,
         size: file.len,
         dev: 0,
@@ -350,6 +396,7 @@ impl<'a> VfsEntryRef<'a> {
         atime: None,
         birthtime: None,
         mtime: None,
+        ctime: None,
         blksize: 0,
         size: 0,
         dev: 0,
@@ -751,14 +798,14 @@ impl deno_io::fs::File for FileBackedVfsFile {
 
 #[derive(Debug)]
 pub struct FileBackedVfs {
-  file: Mutex<Vec<u8>>,
+  vfs_data: Cow<'static, [u8]>,
   fs_root: VfsRoot,
 }
 
 impl FileBackedVfs {
-  pub fn new(file: Vec<u8>, fs_root: VfsRoot) -> Self {
+  pub fn new(data: Cow<'static, [u8]>, fs_root: VfsRoot) -> Self {
     Self {
-      file: Mutex::new(file),
+      vfs_data: data,
       fs_root,
     }
   }
@@ -827,10 +874,15 @@ impl FileBackedVfs {
     Ok(path)
   }
 
-  pub fn read_file_all(&self, file: &VirtualFile) -> std::io::Result<Vec<u8>> {
-    let mut buf = vec![0; file.len as usize];
-    self.read_file(file, 0, &mut buf)?;
-    Ok(buf)
+  pub fn read_file_all(
+    &self,
+    file: &VirtualFile,
+  ) -> std::io::Result<Cow<'static, [u8]>> {
+    let read_range = self.get_read_range(file, 0, file.len)?;
+    match &self.vfs_data {
+      Cow::Borrowed(data) => Ok(Cow::Borrowed(&data[read_range])),
+      Cow::Owned(data) => Ok(Cow::Owned(data[read_range].to_vec())),
+    }
   }
 
   pub fn read_file(
@@ -839,18 +891,27 @@ impl FileBackedVfs {
     pos: u64,
     buf: &mut [u8],
   ) -> std::io::Result<usize> {
-    let data = self.file.lock();
+    let read_range = self.get_read_range(file, pos, buf.len() as u64)?;
+    buf.copy_from_slice(&self.vfs_data[read_range]);
+    Ok(buf.len())
+  }
+
+  fn get_read_range(
+    &self,
+    file: &VirtualFile,
+    pos: u64,
+    len: u64,
+  ) -> std::io::Result<Range<usize>> {
+    let data = &self.vfs_data;
     let start = self.fs_root.start_file_offset + file.offset + pos;
-    let end = start + buf.len() as u64;
+    let end = start + len;
     if end > data.len() as u64 {
       return Err(std::io::Error::new(
         std::io::ErrorKind::UnexpectedEof,
         "unexpected EOF",
       ));
     }
-
-    buf.copy_from_slice(&data[start as usize..end as usize]);
-    Ok(buf.len())
+    Ok(start as usize..end as usize)
   }
 
   pub fn dir_entry(&self, path: &Path) -> std::io::Result<&VirtualDirectory> {
@@ -888,7 +949,7 @@ mod test {
   #[track_caller]
   fn read_file(vfs: &FileBackedVfs, path: &Path) -> String {
     let file = vfs.file_entry(path).unwrap();
-    String::from_utf8(vfs.read_file_all(file).unwrap()).unwrap()
+    String::from_utf8(vfs.read_file_all(file).unwrap().into_owned()).unwrap()
   }
 
   #[test]
@@ -901,20 +962,23 @@ mod test {
     let src_path = src_path.to_path_buf();
     let mut builder = VfsBuilder::new(src_path.clone()).unwrap();
     builder
-      .add_file(&src_path.join("a.txt"), "data".into())
+      .add_file_with_data_inner(&src_path.join("a.txt"), "data".into())
       .unwrap();
     builder
-      .add_file(&src_path.join("b.txt"), "data".into())
+      .add_file_with_data_inner(&src_path.join("b.txt"), "data".into())
       .unwrap();
     assert_eq!(builder.files.len(), 1); // because duplicate data
     builder
-      .add_file(&src_path.join("c.txt"), "c".into())
+      .add_file_with_data_inner(&src_path.join("c.txt"), "c".into())
       .unwrap();
     builder
-      .add_file(&src_path.join("sub_dir").join("d.txt"), "d".into())
+      .add_file_with_data_inner(
+        &src_path.join("sub_dir").join("d.txt"),
+        "d".into(),
+      )
       .unwrap();
     builder
-      .add_file(&src_path.join("e.txt"), "e".into())
+      .add_file_with_data_inner(&src_path.join("e.txt"), "e".into())
       .unwrap();
     builder
       .add_symlink(
@@ -1031,7 +1095,7 @@ mod test {
     (
       dest_path.to_path_buf(),
       FileBackedVfs::new(
-        data,
+        Cow::Owned(data),
         VfsRoot {
           dir: root_dir,
           root_path: dest_path.to_path_buf(),
@@ -1082,7 +1146,7 @@ mod test {
     let temp_path = temp_dir.path().canonicalize();
     let mut builder = VfsBuilder::new(temp_path.to_path_buf()).unwrap();
     builder
-      .add_file(
+      .add_file_with_data_inner(
         temp_path.join("a.txt").as_path(),
         "0123456789".to_string().into_bytes(),
       )