feat(unstable): single checksum per JSR package in the lockfile (#22421)

This changes the lockfile to not store JSR specifiers in the "remote"
section. Instead a single JSR integrity is stored per package in the
lockfile, which is a hash of the version's `x.x.x_meta.json` file, which
contains hashes for every file in the package. The hashes in this file
are then compared against when loading.

Additionally, when using `{ "vendor": true }` in a deno.json, the files
can be modified without causing lockfile errors—the checksum is only
checked when copying into the vendor folder and not afterwards
(eventually we should add this behaviour for non-jsr specifiers as
well). As part of this change, the `vendor` folder creation is not
always automatic in the LSP and running an explicit cache command is
necessary. The code required to track checksums in the LSP would have
been too complex for this PR, so that all goes through deno_graph now.
The vendoring is still automatic when running from the CLI.

13 files changed, 169 insertions, 95 deletions

diff --git a/cli/Cargo.toml b/cli/Cargo.toml
index ca00774ea..3898fb7bb 100644
--- a/cli/Cargo.toml
+++ b/cli/Cargo.toml
@@ -66,17 +66,17 @@ deno_ast = { workspace = true, features = ["bundler", "cjs", "codegen", "proposa
 deno_cache_dir = { workspace = true }
 deno_config = "=0.9.2"
 deno_core = { workspace = true, features = ["include_js_files_for_snapshotting"] }
-deno_doc = { version = "=0.103.0", features = ["html"] }
-deno_emit = "=0.36.0"
-deno_graph = "=0.65.3"
+deno_doc = { version = "=0.107.0", features = ["html"] }
+deno_emit = "=0.37.0"
+deno_graph = "=0.66.0"
 deno_lint = { version = "=0.56.0", features = ["docs"] }
 deno_lockfile.workspace = true
-deno_npm = "=0.16.0"
+deno_npm = "=0.17.0"
 deno_runtime = { workspace = true, features = ["include_js_files_for_snapshotting"] }
 deno_semver = "=0.5.4"
 deno_task_shell = "=0.14.3"
 deno_terminal.workspace = true
-eszip = "=0.62.0"
+eszip = "=0.63.0"
 napi_sym.workspace = true
 
 async-trait.workspace = true
diff --git a/cli/cache/mod.rs b/cli/cache/mod.rs
index 6c48799ce..e9d225146 100644
--- a/cli/cache/mod.rs
+++ b/cli/cache/mod.rs
@@ -196,8 +196,7 @@ impl Loader for FetchCacher {
   fn load(
     &mut self,
     specifier: &ModuleSpecifier,
-    _is_dynamic: bool,
-    cache_setting: deno_graph::source::CacheSetting,
+    options: deno_graph::source::LoadOptions,
   ) -> LoadFuture {
     use deno_graph::source::CacheSetting as LoaderCacheSetting;
 
@@ -222,7 +221,7 @@ impl Loader for FetchCacher {
     let specifier = specifier.clone();
 
     async move {
-      let maybe_cache_setting = match cache_setting {
+      let maybe_cache_setting = match options.cache_setting {
         LoaderCacheSetting::Use => None,
         LoaderCacheSetting::Reload => {
           if matches!(file_fetcher.cache_setting(), CacheSetting::Only) {
@@ -240,6 +239,7 @@ impl Loader for FetchCacher {
           permissions,
           maybe_accept: None,
           maybe_cache_setting: maybe_cache_setting.as_ref(),
+          maybe_checksum: options.maybe_checksum,
         })
         .await
         .map(|file| {
@@ -269,7 +269,7 @@ impl Loader for FetchCacher {
           let error_class_name = get_error_class_name(&err);
           match error_class_name {
             "NotFound" => Ok(None),
-            "NotCached" if cache_setting == LoaderCacheSetting::Only => Ok(None),
+            "NotCached" if options.cache_setting == LoaderCacheSetting::Only => Ok(None),
             _ => Err(err),
           }
         })
diff --git a/cli/factory.rs b/cli/factory.rs
index 2236e6090..cccbecbf1 100644
--- a/cli/factory.rs
+++ b/cli/factory.rs
@@ -66,7 +66,6 @@ use deno_runtime::deno_node::NodeResolver;
 use deno_runtime::deno_tls::RootCertStoreProvider;
 use deno_runtime::deno_web::BlobStore;
 use deno_runtime::inspector_server::InspectorServer;
-use deno_semver::package::PackageNv;
 use import_map::ImportMap;
 use log::warn;
 use std::future::Future;
@@ -381,16 +380,6 @@ impl CliFactory {
             no_npm,
             no_config: self.options.no_config(),
             config,
-            nv_to_jsr_url: |nv| {
-              let nv = PackageNv::from_str(nv).ok()?;
-              Some(
-                deno_graph::source::recommended_registry_package_url(
-                  crate::args::jsr_url(),
-                  &nv,
-                )
-                .to_string(),
-              )
-            },
           },
         );
       }
diff --git a/cli/file_fetcher.rs b/cli/file_fetcher.rs
index 8f4d3feab..a74a14a3f 100644
--- a/cli/file_fetcher.rs
+++ b/cli/file_fetcher.rs
@@ -24,6 +24,7 @@ use deno_core::futures::future::FutureExt;
 use deno_core::parking_lot::Mutex;
 use deno_core::url::Url;
 use deno_core::ModuleSpecifier;
+use deno_graph::source::LoaderChecksum;
 use deno_runtime::deno_fetch::reqwest::header::HeaderValue;
 use deno_runtime::deno_fetch::reqwest::header::ACCEPT;
 use deno_runtime::deno_fetch::reqwest::header::AUTHORIZATION;
@@ -146,6 +147,7 @@ pub struct FetchOptions<'a> {
   pub permissions: PermissionsContainer,
   pub maybe_accept: Option<&'a str>,
   pub maybe_cache_setting: Option<&'a CacheSetting>,
+  pub maybe_checksum: Option<LoaderChecksum>,
 }
 
 /// A structure for resolving, fetching and caching source files.
@@ -199,6 +201,7 @@ impl FileFetcher {
   pub fn fetch_cached(
     &self,
     specifier: &ModuleSpecifier,
+    maybe_checksum: Option<LoaderChecksum>,
     redirect_limit: i64,
   ) -> Result<Option<File>, AnyError> {
     debug!("FileFetcher::fetch_cached - specifier: {}", specifier);
@@ -207,16 +210,22 @@ impl FileFetcher {
     }
 
     let cache_key = self.http_cache.cache_item_key(specifier)?; // compute this once
-    let Some(metadata) = self.http_cache.read_metadata(&cache_key)? else {
+    let Some(headers) = self.http_cache.read_headers(&cache_key)? else {
       return Ok(None);
     };
-    let headers = metadata.headers;
     if let Some(redirect_to) = headers.get("location") {
       let redirect =
         deno_core::resolve_import(redirect_to, specifier.as_str())?;
-      return self.fetch_cached(&redirect, redirect_limit - 1);
+      return self.fetch_cached(&redirect, maybe_checksum, redirect_limit - 1);
     }
-    let Some(bytes) = self.http_cache.read_file_bytes(&cache_key)? else {
+    let Some(bytes) = self.http_cache.read_file_bytes(
+      &cache_key,
+      maybe_checksum
+        .as_ref()
+        .map(|c| deno_cache_dir::Checksum::new(c.as_str())),
+      deno_cache_dir::GlobalToLocalCopy::Allow,
+    )?
+    else {
       return Ok(None);
     };
 
@@ -282,6 +291,7 @@ impl FileFetcher {
     redirect_limit: i64,
     maybe_accept: Option<String>,
     cache_setting: &CacheSetting,
+    maybe_checksum: Option<LoaderChecksum>,
   ) -> Pin<Box<dyn Future<Output = Result<File, AnyError>> + Send>> {
     debug!("FileFetcher::fetch_remote() - specifier: {}", specifier);
     if redirect_limit < 0 {
@@ -294,7 +304,8 @@ impl FileFetcher {
     }
 
     if self.should_use_cache(specifier, cache_setting) {
-      match self.fetch_cached(specifier, redirect_limit) {
+      match self.fetch_cached(specifier, maybe_checksum.clone(), redirect_limit)
+      {
         Ok(Some(file)) => {
           return futures::future::ok(file).boxed();
         }
@@ -331,8 +342,8 @@ impl FileFetcher {
       .http_cache
       .cache_item_key(specifier)
       .ok()
-      .and_then(|key| self.http_cache.read_metadata(&key).ok().flatten())
-      .and_then(|metadata| metadata.headers.get("etag").cloned());
+      .and_then(|key| self.http_cache.read_headers(&key).ok().flatten())
+      .and_then(|headers| headers.get("etag").cloned());
     let maybe_auth_token = self.auth_tokens.get(specifier);
     let specifier = specifier.clone();
     let client = self.http_client.clone();
@@ -376,7 +387,9 @@ impl FileFetcher {
         .await?
         {
           FetchOnceResult::NotModified => {
-            let file = file_fetcher.fetch_cached(&specifier, 10)?.unwrap();
+            let file = file_fetcher
+              .fetch_cached(&specifier, maybe_checksum, 10)?
+              .unwrap();
             Ok(file)
           }
           FetchOnceResult::Redirect(redirect_url, headers) => {
@@ -388,6 +401,7 @@ impl FileFetcher {
                 redirect_limit - 1,
                 maybe_accept,
                 &cache_setting,
+                maybe_checksum,
               )
               .await
           }
@@ -395,6 +409,9 @@ impl FileFetcher {
             file_fetcher
               .http_cache
               .set(&specifier, headers.clone(), &bytes)?;
+            if let Some(checksum) = &maybe_checksum {
+              checksum.check_source(&bytes)?;
+            }
             Ok(File {
               specifier,
               maybe_headers: Some(headers),
@@ -438,15 +455,16 @@ impl FileFetcher {
         let Ok(cache_key) = self.http_cache.cache_item_key(specifier) else {
           return false;
         };
-        let Ok(Some(metadata)) = self.http_cache.read_metadata(&cache_key)
+        let Ok(Some(headers)) = self.http_cache.read_headers(&cache_key) else {
+          return false;
+        };
+        let Ok(Some(download_time)) =
+          self.http_cache.read_download_time(&cache_key)
         else {
           return false;
         };
-        let cache_semantics = CacheSemantics::new(
-          metadata.headers,
-          metadata.time,
-          SystemTime::now(),
-        );
+        let cache_semantics =
+          CacheSemantics::new(headers, download_time, SystemTime::now());
         cache_semantics.should_use()
       }
       CacheSetting::ReloadSome(list) => {
@@ -482,6 +500,7 @@ impl FileFetcher {
         permissions,
         maybe_accept: None,
         maybe_cache_setting: None,
+        maybe_checksum: None,
       })
       .await
   }
@@ -517,6 +536,7 @@ impl FileFetcher {
           10,
           options.maybe_accept.map(String::from),
           options.maybe_cache_setting.unwrap_or(&self.cache_setting),
+          options.maybe_checksum,
         )
         .await
     }
@@ -728,6 +748,7 @@ mod tests {
         1,
         None,
         &file_fetcher.cache_setting,
+        None,
       )
       .await;
     let cache_key = file_fetcher.http_cache.cache_item_key(specifier).unwrap();
@@ -735,10 +756,9 @@ mod tests {
       result.unwrap(),
       file_fetcher
         .http_cache
-        .read_metadata(&cache_key)
-        .unwrap()
+        .read_headers(&cache_key)
         .unwrap()
-        .headers,
+        .unwrap(),
     )
   }
 
@@ -899,18 +919,11 @@ mod tests {
 
     let cache_item_key =
       file_fetcher.http_cache.cache_item_key(&specifier).unwrap();
-    let mut metadata = file_fetcher
-      .http_cache
-      .read_metadata(&cache_item_key)
-      .unwrap()
-      .unwrap();
-    metadata.headers = HashMap::new();
-    metadata
-      .headers
-      .insert("content-type".to_string(), "text/javascript".to_string());
+    let mut headers = HashMap::new();
+    headers.insert("content-type".to_string(), "text/javascript".to_string());
     file_fetcher
       .http_cache
-      .set(&specifier, metadata.headers.clone(), file.source.as_bytes())
+      .set(&specifier, headers.clone(), file.source.as_bytes())
       .unwrap();
 
     let result = file_fetcher_01
@@ -926,20 +939,17 @@ mod tests {
     // the value above.
     assert_eq!(file.media_type, MediaType::JavaScript);
 
-    let headers = file_fetcher_02
+    let headers2 = file_fetcher_02
       .http_cache
-      .read_metadata(&cache_item_key)
+      .read_headers(&cache_item_key)
       .unwrap()
-      .unwrap()
-      .headers;
-    assert_eq!(headers.get("content-type").unwrap(), "text/javascript");
-    metadata.headers = HashMap::new();
-    metadata
-      .headers
-      .insert("content-type".to_string(), "application/json".to_string());
+      .unwrap();
+    assert_eq!(headers2.get("content-type").unwrap(), "text/javascript");
+    headers = HashMap::new();
+    headers.insert("content-type".to_string(), "application/json".to_string());
     file_fetcher_02
       .http_cache
-      .set(&specifier, metadata.headers.clone(), file.source.as_bytes())
+      .set(&specifier, headers.clone(), file.source.as_bytes())
       .unwrap();
 
     let result = file_fetcher_02
@@ -1013,7 +1023,12 @@ mod tests {
           .unwrap(),
         file_fetcher
           .http_cache
-          .read_metadata(&cache_key)
+          .read_headers(&cache_key)
+          .unwrap()
+          .unwrap(),
+        file_fetcher
+          .http_cache
+          .read_download_time(&cache_key)
           .unwrap()
           .unwrap(),
       )
@@ -1045,7 +1060,12 @@ mod tests {
           .unwrap(),
         file_fetcher
           .http_cache
-          .read_metadata(&cache_key)
+          .read_headers(&cache_key)
+          .unwrap()
+          .unwrap(),
+        file_fetcher
+          .http_cache
+          .read_download_time(&cache_key)
           .unwrap()
           .unwrap(),
       )
@@ -1182,7 +1202,12 @@ mod tests {
           .unwrap(),
         file_fetcher
           .http_cache
-          .read_metadata(&cache_key)
+          .read_headers(&cache_key)
+          .unwrap()
+          .unwrap(),
+        file_fetcher
+          .http_cache
+          .read_download_time(&cache_key)
           .unwrap()
           .unwrap(),
       )
@@ -1216,7 +1241,12 @@ mod tests {
           .unwrap(),
         file_fetcher
           .http_cache
-          .read_metadata(&cache_key)
+          .read_headers(&cache_key)
+          .unwrap()
+          .unwrap(),
+        file_fetcher
+          .http_cache
+          .read_download_time(&cache_key)
           .unwrap()
           .unwrap(),
       )
@@ -1240,6 +1270,7 @@ mod tests {
         2,
         None,
         &file_fetcher.cache_setting,
+        None,
       )
       .await;
     assert!(result.is_ok());
@@ -1251,14 +1282,15 @@ mod tests {
         1,
         None,
         &file_fetcher.cache_setting,
+        None,
       )
       .await;
     assert!(result.is_err());
 
-    let result = file_fetcher.fetch_cached(&specifier, 2);
+    let result = file_fetcher.fetch_cached(&specifier, None, 2);
     assert!(result.is_ok());
 
-    let result = file_fetcher.fetch_cached(&specifier, 1);
+    let result = file_fetcher.fetch_cached(&specifier, None, 1);
     assert!(result.is_err());
   }
 
@@ -2072,7 +2104,11 @@ mod tests {
     let cache_key = file_fetcher.http_cache.cache_item_key(url).unwrap();
     let bytes = file_fetcher
       .http_cache
-      .read_file_bytes(&cache_key)
+      .read_file_bytes(
+        &cache_key,
+        None,
+        deno_cache_dir::GlobalToLocalCopy::Allow,
+      )
       .unwrap()
       .unwrap();
     String::from_utf8(bytes).unwrap()
@@ -2086,10 +2122,9 @@ mod tests {
     let cache_key = file_fetcher.http_cache.cache_item_key(url).unwrap();
     file_fetcher
       .http_cache
-      .read_metadata(&cache_key)
+      .read_headers(&cache_key)
       .unwrap()
       .unwrap()
-      .headers
       .remove("location")
   }
 }
diff --git a/cli/graph_util.rs b/cli/graph_util.rs
index 3633784b8..09f0db9e6 100644
--- a/cli/graph_util.rs
+++ b/cli/graph_util.rs
@@ -1,5 +1,6 @@
 // Copyright 2018-2024 the Deno authors. All rights reserved. MIT license.
 
+use crate::args::jsr_url;
 use crate::args::CliOptions;
 use crate::args::Lockfile;
 use crate::args::TsTypeLib;
@@ -174,6 +175,18 @@ pub fn graph_lock_or_exit(graph: &ModuleGraph, lockfile: &mut Lockfile) {
       Module::Json(module) => &module.source,
       Module::Node(_) | Module::Npm(_) | Module::External(_) => continue,
     };
+
+    // skip over any specifiers in JSR packages because those
+    // are enforced via the integrity
+    if deno_graph::source::recommended_registry_package_url_to_nv(
+      jsr_url(),
+      module.specifier(),
+    )
+    .is_some()
+    {
+      continue;
+    }
+
     if !lockfile.check_or_insert_remote(module.specifier().as_str(), source) {
       let err = format!(
         concat!(
@@ -475,6 +488,19 @@ impl ModuleGraphBuilder {
             }
           }
         }
+        for (nv, value) in &lockfile.content.packages.jsr {
+          if let Ok(nv) = PackageNv::from_str(nv) {
+            graph
+              .packages
+              .add_manifest_checksum(nv, value.integrity.clone())
+              .map_err(|err| deno_lockfile::IntegrityCheckFailedError {
+                package_display_id: format!("jsr:{}", err.nv),
+                actual: err.actual,
+                expected: err.expected,
+                filename: lockfile.filename.display().to_string(),
+              })?;
+          }
+        }
       }
     }
 
@@ -504,9 +530,14 @@ impl ModuleGraphBuilder {
             format!("jsr:{}", to),
           );
         }
-        for (name, deps) in graph.packages.package_deps() {
-          lockfile
-            .insert_package_deps(name.to_string(), deps.map(|s| s.to_string()));
+        for (name, checksum, deps) in
+          graph.packages.packages_with_checksum_and_deps()
+        {
+          lockfile.insert_package(
+            name.to_string(),
+            checksum.clone(),
+            deps.map(|s| s.to_string()),
+          );
         }
       }
     }
diff --git a/cli/lsp/cache.rs b/cli/lsp/cache.rs
index eec6433a2..e0034207d 100644
--- a/cli/lsp/cache.rs
+++ b/cli/lsp/cache.rs
@@ -11,6 +11,16 @@ use std::path::Path;
 use std::sync::Arc;
 use std::time::SystemTime;
 
+/// In the LSP, we disallow the cache from automatically copying from
+/// the global cache to the local cache for technical reasons.
+///
+/// 1. We need to verify the checksums from the lockfile are correct when
+///    moving from the global to the local cache.
+/// 2. We need to verify the checksums for JSR https specifiers match what
+///    is found in the package's manifest.
+pub const LSP_DISALLOW_GLOBAL_TO_LOCAL_COPY: deno_cache_dir::GlobalToLocalCopy =
+  deno_cache_dir::GlobalToLocalCopy::Disallow;
+
 pub fn calculate_fs_version(
   cache: &Arc<dyn HttpCache>,
   specifier: &ModuleSpecifier,
@@ -123,8 +133,8 @@ impl CacheMetadata {
       return None;
     }
     let cache_key = self.cache.cache_item_key(specifier).ok()?;
-    let specifier_metadata = self.cache.read_metadata(&cache_key).ok()??;
-    let values = Arc::new(parse_metadata(&specifier_metadata.headers));
+    let headers = self.cache.read_headers(&cache_key).ok()??;
+    let values = Arc::new(parse_metadata(&headers));
     let version = calculate_fs_version_in_cache(&self.cache, specifier);
     let mut metadata_map = self.metadata.lock();
     let metadata = Metadata { values, version };
diff --git a/cli/lsp/documents.rs b/cli/lsp/documents.rs
index c58a392d5..125307757 100644
--- a/cli/lsp/documents.rs
+++ b/cli/lsp/documents.rs
@@ -2,6 +2,7 @@
 
 use super::cache::calculate_fs_version;
 use super::cache::calculate_fs_version_at_path;
+use super::cache::LSP_DISALLOW_GLOBAL_TO_LOCAL_COPY;
 use super::jsr_resolver::JsrResolver;
 use super::language_server::StateNpmSnapshot;
 use super::text::LineIndex;
@@ -736,12 +737,7 @@ impl RedirectResolver {
   ) -> Option<ModuleSpecifier> {
     if redirect_limit > 0 {
       let cache_key = self.cache.cache_item_key(specifier).ok()?;
-      let headers = self
-        .cache
-        .read_metadata(&cache_key)
-        .ok()
-        .flatten()
-        .map(|m| m.headers)?;
+      let headers = self.cache.read_headers(&cache_key).ok().flatten()?;
       if let Some(location) = headers.get("location") {
         let redirect =
           deno_core::resolve_import(location, specifier.as_str()).ok()?;
@@ -822,12 +818,14 @@ impl FileSystemDocuments {
     } else {
       let fs_version = calculate_fs_version(cache, specifier)?;
       let cache_key = cache.cache_item_key(specifier).ok()?;
-      let bytes = cache.read_file_bytes(&cache_key).ok()??;
-      let specifier_metadata = cache.read_metadata(&cache_key).ok()??;
+      let bytes = cache
+        .read_file_bytes(&cache_key, None, LSP_DISALLOW_GLOBAL_TO_LOCAL_COPY)
+        .ok()??;
+      let specifier_headers = cache.read_headers(&cache_key).ok()??;
       let (_, maybe_charset) =
         deno_graph::source::resolve_media_type_and_charset_from_headers(
           specifier,
-          Some(&specifier_metadata.headers),
+          Some(&specifier_headers),
         );
       let content = deno_graph::source::decode_owned_source(
         specifier,
@@ -835,7 +833,7 @@ impl FileSystemDocuments {
         maybe_charset,
       )
       .ok()?;
-      let maybe_headers = Some(specifier_metadata.headers);
+      let maybe_headers = Some(specifier_headers);
       Document::new(
         specifier.clone(),
         fs_version,
@@ -1826,8 +1824,7 @@ impl<'a> deno_graph::source::Loader for OpenDocumentsGraphLoader<'a> {
   fn load(
     &mut self,
     specifier: &ModuleSpecifier,
-    is_dynamic: bool,
-    cache_setting: deno_graph::source::CacheSetting,
+    options: deno_graph::source::LoadOptions,
   ) -> deno_graph::source::LoadFuture {
     let specifier = if self.unstable_sloppy_imports {
       self
@@ -1839,9 +1836,7 @@ impl<'a> deno_graph::source::Loader for OpenDocumentsGraphLoader<'a> {
 
     match self.load_from_docs(&specifier) {
       Some(fut) => fut,
-      None => self
-        .inner_loader
-        .load(&specifier, is_dynamic, cache_setting),
+      None => self.inner_loader.load(&specifier, options),
     }
   }
 
diff --git a/cli/lsp/jsr_resolver.rs b/cli/lsp/jsr_resolver.rs
index 8243bb0f2..be7bdc0f5 100644
--- a/cli/lsp/jsr_resolver.rs
+++ b/cli/lsp/jsr_resolver.rs
@@ -15,6 +15,8 @@ use deno_semver::package::PackageReq;
 use std::borrow::Cow;
 use std::sync::Arc;
 
+use super::cache::LSP_DISALLOW_GLOBAL_TO_LOCAL_COPY;
+
 #[derive(Debug)]
 pub struct JsrResolver {
   nv_by_req: DashMap<PackageReq, Option<PackageNv>>,
@@ -111,7 +113,13 @@ fn read_cached_package_info(
 ) -> Option<JsrPackageInfo> {
   let meta_url = jsr_url().join(&format!("{}/meta.json", name)).ok()?;
   let meta_cache_item_key = cache.cache_item_key(&meta_url).ok()?;
-  let meta_bytes = cache.read_file_bytes(&meta_cache_item_key).ok()??;
+  let meta_bytes = cache
+    .read_file_bytes(
+      &meta_cache_item_key,
+      None,
+      LSP_DISALLOW_GLOBAL_TO_LOCAL_COPY,
+    )
+    .ok()??;
   serde_json::from_slice::<JsrPackageInfo>(&meta_bytes).ok()
 }
 
@@ -123,12 +131,19 @@ fn read_cached_package_version_info(
     .join(&format!("{}/{}_meta.json", &nv.name, &nv.version))
     .ok()?;
   let meta_cache_item_key = cache.cache_item_key(&meta_url).ok()?;
-  let meta_bytes = cache.read_file_bytes(&meta_cache_item_key).ok()??;
+  let meta_bytes = cache
+    .read_file_bytes(
+      &meta_cache_item_key,
+      None,
+      LSP_DISALLOW_GLOBAL_TO_LOCAL_COPY,
+    )
+    .ok()??;
   // This is a roundabout way of deserializing `JsrPackageVersionInfo`,
   // because we only want the `exports` field and `module_graph` is large.
   let mut info =
     serde_json::from_slice::<serde_json::Value>(&meta_bytes).ok()?;
   Some(JsrPackageVersionInfo {
+    manifest: Default::default(), // not used by the LSP (only caching checks this in deno_graph)
     exports: info.as_object_mut()?.remove("exports")?,
     module_graph: None,
   })
diff --git a/cli/lsp/registries.rs b/cli/lsp/registries.rs
index f4a64c7ee..2b0cae7d2 100644
--- a/cli/lsp/registries.rs
+++ b/cli/lsp/registries.rs
@@ -515,6 +515,7 @@ impl ModuleRegistry {
         permissions: PermissionsContainer::allow_all(),
         maybe_accept: Some("application/vnd.deno.reg.v2+json, application/vnd.deno.reg.v1+json;q=0.9, application/json;q=0.8"),
         maybe_cache_setting: None,
+        maybe_checksum: None,
       })
       .await;
     // if there is an error fetching, we will cache an empty file, so that
diff --git a/cli/tools/coverage/mod.rs b/cli/tools/coverage/mod.rs
index aafef292f..5cc705741 100644
--- a/cli/tools/coverage/mod.rs
+++ b/cli/tools/coverage/mod.rs
@@ -523,7 +523,7 @@ pub async fn cover_files(
       file_fetcher.get_source(&module_specifier)
     } else {
       file_fetcher
-        .fetch_cached(&module_specifier, 10)
+        .fetch_cached(&module_specifier, None, 10)
         .with_context(|| {
           format!("Failed to fetch \"{module_specifier}\" from cache.")
         })?
diff --git a/cli/tools/doc.rs b/cli/tools/doc.rs
index d2cd0c2a2..5044e73d3 100644
--- a/cli/tools/doc.rs
+++ b/cli/tools/doc.rs
@@ -211,9 +211,9 @@ impl deno_doc::html::HrefResolver for DocResolver {
   fn resolve_usage(
     &self,
     _current_specifier: &ModuleSpecifier,
-    current_file: &str,
+    current_file: Option<&str>,
   ) -> Option<String> {
-    Some(current_file.to_string())
+    current_file.map(|f| f.to_string())
   }
 
   fn resolve_source(&self, location: &deno_doc::Location) -> Option<String> {
diff --git a/cli/tools/vendor/test.rs b/cli/tools/vendor/test.rs
index 7910dcf22..6a960c302 100644
--- a/cli/tools/vendor/test.rs
+++ b/cli/tools/vendor/test.rs
@@ -115,8 +115,7 @@ impl Loader for TestLoader {
   fn load(
     &mut self,
     specifier: &ModuleSpecifier,
-    _is_dynamic: bool,
-    _cache_setting: deno_graph::source::CacheSetting,
+    _options: deno_graph::source::LoadOptions,
   ) -> LoadFuture {
     let specifier = self.redirects.get(specifier).unwrap_or(specifier);
     let result = self.files.get(specifier).map(|result| match result {
diff --git a/cli/tsc/mod.rs b/cli/tsc/mod.rs
index 18316b750..f3f974690 100644
--- a/cli/tsc/mod.rs
+++ b/cli/tsc/mod.rs
@@ -904,8 +904,7 @@ mod tests {
     fn load(
       &mut self,
       specifier: &ModuleSpecifier,
-      _is_dynamic: bool,
-      _cache_setting: deno_graph::source::CacheSetting,
+      _options: deno_graph::source::LoadOptions,
     ) -> deno_graph::source::LoadFuture {
       let specifier_text = specifier
         .to_string()