refactor(permissions): add PermissionsContainer struct for internal mutability (#17134)

Turns out we were cloning permissions which after prompting were discarded,
so the state of permissions was never preserved. To handle that we need to store
all permissions behind "Arc<Mutex<>>" (because there are situations where we
need to send them to other thread).

Testing and benching code still uses "Permissions" in most places - it's undesirable
to share the same permission set between various test/bench files - otherwise
granting or revoking permissions in one file would influence behavior of other test
files.

18 files changed, 172 insertions, 117 deletions

diff --git a/cli/build.rs b/cli/build.rs
index faeaed073..b4acc0d1d 100644
--- a/cli/build.rs
+++ b/cli/build.rs
@@ -7,7 +7,7 @@ use std::path::PathBuf;
 use deno_core::snapshot_util::*;
 use deno_core::Extension;
 use deno_runtime::deno_cache::SqliteBackedCache;
-use deno_runtime::permissions::Permissions;
+use deno_runtime::permissions::PermissionsContainer;
 use deno_runtime::*;
 
 mod ts {
@@ -294,13 +294,13 @@ fn create_cli_snapshot(snapshot_path: PathBuf, files: Vec<PathBuf>) {
     deno_console::init(),
     deno_url::init(),
     deno_tls::init(),
-    deno_web::init::<Permissions>(
+    deno_web::init::<PermissionsContainer>(
       deno_web::BlobStore::default(),
       Default::default(),
     ),
-    deno_fetch::init::<Permissions>(Default::default()),
+    deno_fetch::init::<PermissionsContainer>(Default::default()),
     deno_cache::init::<SqliteBackedCache>(None),
-    deno_websocket::init::<Permissions>("".to_owned(), None, None),
+    deno_websocket::init::<PermissionsContainer>("".to_owned(), None, None),
     deno_webstorage::init(None),
     deno_crypto::init(None),
     deno_webgpu::init(false),
@@ -308,15 +308,15 @@ fn create_cli_snapshot(snapshot_path: PathBuf, files: Vec<PathBuf>) {
       deno_broadcast_channel::InMemoryBroadcastChannel::default(),
       false, // No --unstable.
     ),
-    deno_node::init::<Permissions>(None), // No --unstable.
-    deno_ffi::init::<Permissions>(false),
-    deno_net::init::<Permissions>(
+    deno_node::init::<PermissionsContainer>(None), // No --unstable.
+    deno_ffi::init::<PermissionsContainer>(false),
+    deno_net::init::<PermissionsContainer>(
       None, false, // No --unstable.
       None,
     ),
-    deno_napi::init::<Permissions>(false),
+    deno_napi::init::<PermissionsContainer>(false),
     deno_http::init(),
-    deno_flash::init::<Permissions>(false), // No --unstable
+    deno_flash::init::<PermissionsContainer>(false), // No --unstable
   ];
 
   create_snapshot(CreateSnapshotOptions {
diff --git a/cli/cache/mod.rs b/cli/cache/mod.rs
index 68bf1e4c6..d2ad1b20a 100644
--- a/cli/cache/mod.rs
+++ b/cli/cache/mod.rs
@@ -11,7 +11,7 @@ use deno_graph::source::CacheInfo;
 use deno_graph::source::LoadFuture;
 use deno_graph::source::LoadResponse;
 use deno_graph::source::Loader;
-use deno_runtime::permissions::Permissions;
+use deno_runtime::permissions::PermissionsContainer;
 use std::sync::Arc;
 
 mod check;
@@ -42,17 +42,17 @@ pub const CACHE_PERM: u32 = 0o644;
 /// a concise interface to the DENO_DIR when building module graphs.
 pub struct FetchCacher {
   emit_cache: EmitCache,
-  dynamic_permissions: Permissions,
+  dynamic_permissions: PermissionsContainer,
   file_fetcher: Arc<FileFetcher>,
-  root_permissions: Permissions,
+  root_permissions: PermissionsContainer,
 }
 
 impl FetchCacher {
   pub fn new(
     emit_cache: EmitCache,
     file_fetcher: FileFetcher,
-    root_permissions: Permissions,
-    dynamic_permissions: Permissions,
+    root_permissions: PermissionsContainer,
+    dynamic_permissions: PermissionsContainer,
   ) -> Self {
     let file_fetcher = Arc::new(file_fetcher);
 
@@ -104,7 +104,7 @@ impl Loader for FetchCacher {
     }
 
     let specifier = specifier.clone();
-    let mut permissions = if is_dynamic {
+    let permissions = if is_dynamic {
       self.dynamic_permissions.clone()
     } else {
       self.root_permissions.clone()
@@ -113,7 +113,7 @@ impl Loader for FetchCacher {
 
     async move {
       file_fetcher
-        .fetch(&specifier, &mut permissions)
+        .fetch(&specifier, permissions)
         .await
         .map_or_else(
           |err| {
diff --git a/cli/file_fetcher.rs b/cli/file_fetcher.rs
index cc83e6f5f..2376133f5 100644
--- a/cli/file_fetcher.rs
+++ b/cli/file_fetcher.rs
@@ -31,7 +31,7 @@ use deno_runtime::deno_fetch::reqwest::header::AUTHORIZATION;
 use deno_runtime::deno_fetch::reqwest::header::IF_NONE_MATCH;
 use deno_runtime::deno_fetch::reqwest::StatusCode;
 use deno_runtime::deno_web::BlobStore;
-use deno_runtime::permissions::Permissions;
+use deno_runtime::permissions::PermissionsContainer;
 use log::debug;
 use std::borrow::Borrow;
 use std::collections::HashMap;
@@ -406,7 +406,7 @@ impl FileFetcher {
   fn fetch_remote(
     &self,
     specifier: &ModuleSpecifier,
-    permissions: &mut Permissions,
+    permissions: PermissionsContainer,
     redirect_limit: i64,
     maybe_accept: Option<String>,
   ) -> Pin<Box<dyn Future<Output = Result<File, AnyError>> + Send>> {
@@ -461,7 +461,6 @@ impl FileFetcher {
     };
     let maybe_auth_token = self.auth_tokens.get(specifier);
     let specifier = specifier.clone();
-    let mut permissions = permissions.clone();
     let client = self.http_client.clone();
     let file_fetcher = self.clone();
     // A single pass of fetch either yields code or yields a redirect.
@@ -487,7 +486,7 @@ impl FileFetcher {
           file_fetcher
             .fetch_remote(
               &redirect_url,
-              &mut permissions,
+              permissions,
               redirect_limit - 1,
               maybe_accept,
             )
@@ -547,7 +546,7 @@ impl FileFetcher {
   pub async fn fetch(
     &self,
     specifier: &ModuleSpecifier,
-    permissions: &mut Permissions,
+    permissions: PermissionsContainer,
   ) -> Result<File, AnyError> {
     debug!("FileFetcher::fetch() - specifier: {}", specifier);
     self.fetch_with_accept(specifier, permissions, None).await
@@ -556,7 +555,7 @@ impl FileFetcher {
   pub async fn fetch_with_accept(
     &self,
     specifier: &ModuleSpecifier,
-    permissions: &mut Permissions,
+    permissions: PermissionsContainer,
     maybe_accept: Option<&str>,
   ) -> Result<File, AnyError> {
     let scheme = get_validated_scheme(specifier)?;
@@ -797,7 +796,7 @@ mod tests {
   async fn test_fetch(specifier: &ModuleSpecifier) -> (File, FileFetcher) {
     let (file_fetcher, _) = setup(CacheSetting::ReloadAll, None);
     let result = file_fetcher
-      .fetch(specifier, &mut Permissions::allow_all())
+      .fetch(specifier, PermissionsContainer::allow_all())
       .await;
     assert!(result.is_ok());
     (result.unwrap(), file_fetcher)
@@ -809,7 +808,7 @@ mod tests {
     let _http_server_guard = test_util::http_server();
     let (file_fetcher, _) = setup(CacheSetting::ReloadAll, None);
     let result: Result<File, AnyError> = file_fetcher
-      .fetch_remote(specifier, &mut Permissions::allow_all(), 1, None)
+      .fetch_remote(specifier, PermissionsContainer::allow_all(), 1, None)
       .await;
     assert!(result.is_ok());
     let (_, headers, _) = file_fetcher.http_cache.get(specifier).unwrap();
@@ -1053,7 +1052,7 @@ mod tests {
     file_fetcher.insert_cached(file.clone());
 
     let result = file_fetcher
-      .fetch(&specifier, &mut Permissions::allow_all())
+      .fetch(&specifier, PermissionsContainer::allow_all())
       .await;
     assert!(result.is_ok());
     let result_file = result.unwrap();
@@ -1069,7 +1068,7 @@ mod tests {
         .unwrap();
 
     let result = file_fetcher
-      .fetch(&specifier, &mut Permissions::allow_all())
+      .fetch(&specifier, PermissionsContainer::allow_all())
       .await;
     assert!(result.is_ok());
 
@@ -1098,7 +1097,7 @@ mod tests {
     let specifier = resolve_url("data:application/typescript;base64,ZXhwb3J0IGNvbnN0IGEgPSAiYSI7CgpleHBvcnQgZW51bSBBIHsKICBBLAogIEIsCiAgQywKfQo=").unwrap();
 
     let result = file_fetcher
-      .fetch(&specifier, &mut Permissions::allow_all())
+      .fetch(&specifier, PermissionsContainer::allow_all())
       .await;
     assert!(result.is_ok());
     let file = result.unwrap();
@@ -1130,7 +1129,7 @@ mod tests {
     );
 
     let result = file_fetcher
-      .fetch(&specifier, &mut Permissions::allow_all())
+      .fetch(&specifier, PermissionsContainer::allow_all())
       .await;
     assert!(result.is_ok());
     let file = result.unwrap();
@@ -1153,7 +1152,7 @@ mod tests {
       resolve_url_or_path("http://localhost:4545/subdir/mod2.ts").unwrap();
 
     let result = file_fetcher
-      .fetch(&specifier, &mut Permissions::allow_all())
+      .fetch(&specifier, PermissionsContainer::allow_all())
       .await;
     assert!(result.is_ok());
     let file = result.unwrap();
@@ -1175,7 +1174,7 @@ mod tests {
     metadata.write(&cache_filename).unwrap();
 
     let result = file_fetcher_01
-      .fetch(&specifier, &mut Permissions::allow_all())
+      .fetch(&specifier, PermissionsContainer::allow_all())
       .await;
     assert!(result.is_ok());
     let file = result.unwrap();
@@ -1196,7 +1195,7 @@ mod tests {
     metadata.write(&cache_filename).unwrap();
 
     let result = file_fetcher_02
-      .fetch(&specifier, &mut Permissions::allow_all())
+      .fetch(&specifier, PermissionsContainer::allow_all())
       .await;
     assert!(result.is_ok());
     let file = result.unwrap();
@@ -1219,7 +1218,7 @@ mod tests {
     )
     .unwrap();
     let result = file_fetcher
-      .fetch(&specifier, &mut Permissions::allow_all())
+      .fetch(&specifier, PermissionsContainer::allow_all())
       .await;
     assert!(result.is_ok());
     let file = result.unwrap();
@@ -1252,7 +1251,7 @@ mod tests {
       .unwrap();
 
     let result = file_fetcher_01
-      .fetch(&specifier, &mut Permissions::allow_all())
+      .fetch(&specifier, PermissionsContainer::allow_all())
       .await;
     assert!(result.is_ok());
 
@@ -1271,7 +1270,7 @@ mod tests {
     )
     .unwrap();
     let result = file_fetcher_02
-      .fetch(&specifier, &mut Permissions::allow_all())
+      .fetch(&specifier, PermissionsContainer::allow_all())
       .await;
     assert!(result.is_ok());
 
@@ -1303,7 +1302,7 @@ mod tests {
       .unwrap();
 
     let result = file_fetcher
-      .fetch(&specifier, &mut Permissions::allow_all())
+      .fetch(&specifier, PermissionsContainer::allow_all())
       .await;
     assert!(result.is_ok());
     let file = result.unwrap();
@@ -1356,7 +1355,7 @@ mod tests {
       .unwrap();
 
     let result = file_fetcher
-      .fetch(&specifier, &mut Permissions::allow_all())
+      .fetch(&specifier, PermissionsContainer::allow_all())
       .await;
     assert!(result.is_ok());
     let file = result.unwrap();
@@ -1422,7 +1421,7 @@ mod tests {
       .unwrap();
 
     let result = file_fetcher_01
-      .fetch(&specifier, &mut Permissions::allow_all())
+      .fetch(&specifier, PermissionsContainer::allow_all())
       .await;
     assert!(result.is_ok());
 
@@ -1442,7 +1441,7 @@ mod tests {
     )
     .unwrap();
     let result = file_fetcher_02
-      .fetch(&redirected_specifier, &mut Permissions::allow_all())
+      .fetch(&redirected_specifier, PermissionsContainer::allow_all())
       .await;
     assert!(result.is_ok());
 
@@ -1464,12 +1463,12 @@ mod tests {
         .unwrap();
 
     let result = file_fetcher
-      .fetch_remote(&specifier, &mut Permissions::allow_all(), 2, None)
+      .fetch_remote(&specifier, PermissionsContainer::allow_all(), 2, None)
       .await;
     assert!(result.is_ok());
 
     let result = file_fetcher
-      .fetch_remote(&specifier, &mut Permissions::allow_all(), 1, None)
+      .fetch_remote(&specifier, PermissionsContainer::allow_all(), 1, None)
       .await;
     assert!(result.is_err());
 
@@ -1501,7 +1500,7 @@ mod tests {
       .unwrap();
 
     let result = file_fetcher
-      .fetch(&specifier, &mut Permissions::allow_all())
+      .fetch(&specifier, PermissionsContainer::allow_all())
       .await;
     assert!(result.is_ok());
     let file = result.unwrap();
@@ -1545,7 +1544,7 @@ mod tests {
       resolve_url("http://localhost:4545/run/002_hello.ts").unwrap();
 
     let result = file_fetcher
-      .fetch(&specifier, &mut Permissions::allow_all())
+      .fetch(&specifier, PermissionsContainer::allow_all())
       .await;
     assert!(result.is_err());
     let err = result.unwrap_err();
@@ -1580,7 +1579,7 @@ mod tests {
       resolve_url("http://localhost:4545/run/002_hello.ts").unwrap();
 
     let result = file_fetcher_01
-      .fetch(&specifier, &mut Permissions::allow_all())
+      .fetch(&specifier, PermissionsContainer::allow_all())
       .await;
     assert!(result.is_err());
     let err = result.unwrap_err();
@@ -1588,12 +1587,12 @@ mod tests {
     assert_eq!(err.to_string(), "Specifier not found in cache: \"http://localhost:4545/run/002_hello.ts\", --cached-only is specified.");
 
     let result = file_fetcher_02
-      .fetch(&specifier, &mut Permissions::allow_all())
+      .fetch(&specifier, PermissionsContainer::allow_all())
       .await;
     assert!(result.is_ok());
 
     let result = file_fetcher_01
-      .fetch(&specifier, &mut Permissions::allow_all())
+      .fetch(&specifier, PermissionsContainer::allow_all())
       .await;
     assert!(result.is_ok());
   }
@@ -1606,7 +1605,7 @@ mod tests {
       resolve_url_or_path(&fixture_path.to_string_lossy()).unwrap();
     fs::write(fixture_path.clone(), r#"console.log("hello deno");"#).unwrap();
     let result = file_fetcher
-      .fetch(&specifier, &mut Permissions::allow_all())
+      .fetch(&specifier, PermissionsContainer::allow_all())
       .await;
     assert!(result.is_ok());
     let file = result.unwrap();
@@ -1614,7 +1613,7 @@ mod tests {
 
     fs::write(fixture_path, r#"console.log("goodbye deno");"#).unwrap();
     let result = file_fetcher
-      .fetch(&specifier, &mut Permissions::allow_all())
+      .fetch(&specifier, PermissionsContainer::allow_all())
       .await;
     assert!(result.is_ok());
     let file = result.unwrap();
@@ -1630,7 +1629,7 @@ mod tests {
     let specifier =
       ModuleSpecifier::parse("http://localhost:4545/dynamic").unwrap();
     let result = file_fetcher
-      .fetch(&specifier, &mut Permissions::allow_all())
+      .fetch(&specifier, PermissionsContainer::allow_all())
       .await;
     assert!(result.is_ok());
     let file = result.unwrap();
@@ -1639,7 +1638,7 @@ mod tests {
     let (file_fetcher, _) =
       setup(CacheSetting::RespectHeaders, Some(temp_dir.clone()));
     let result = file_fetcher
-      .fetch(&specifier, &mut Permissions::allow_all())
+      .fetch(&specifier, PermissionsContainer::allow_all())
       .await;
     assert!(result.is_ok());
     let file = result.unwrap();
@@ -1657,7 +1656,7 @@ mod tests {
     let specifier =
       ModuleSpecifier::parse("http://localhost:4545/dynamic_cache").unwrap();
     let result = file_fetcher
-      .fetch(&specifier, &mut Permissions::allow_all())
+      .fetch(&specifier, PermissionsContainer::allow_all())
       .await;
     assert!(result.is_ok());
     let file = result.unwrap();
@@ -1666,7 +1665,7 @@ mod tests {
     let (file_fetcher, _) =
       setup(CacheSetting::RespectHeaders, Some(temp_dir.clone()));
     let result = file_fetcher
-      .fetch(&specifier, &mut Permissions::allow_all())
+      .fetch(&specifier, PermissionsContainer::allow_all())
       .await;
     assert!(result.is_ok());
     let file = result.unwrap();
diff --git a/cli/graph_util.rs b/cli/graph_util.rs
index d815e3311..812701892 100644
--- a/cli/graph_util.rs
+++ b/cli/graph_util.rs
@@ -28,7 +28,7 @@ use deno_graph::ModuleGraphError;
 use deno_graph::ModuleKind;
 use deno_graph::Range;
 use deno_graph::Resolved;
-use deno_runtime::permissions::Permissions;
+use deno_runtime::permissions::PermissionsContainer;
 use std::collections::BTreeMap;
 use std::collections::HashMap;
 use std::collections::HashSet;
@@ -514,8 +514,8 @@ pub async fn create_graph_and_maybe_check(
   let mut cache = cache::FetchCacher::new(
     ps.emit_cache.clone(),
     ps.file_fetcher.clone(),
-    Permissions::allow_all(),
-    Permissions::allow_all(),
+    PermissionsContainer::allow_all(),
+    PermissionsContainer::allow_all(),
   );
   let maybe_imports = ps.options.to_maybe_imports()?;
   let maybe_cli_resolver = CliResolver::maybe_new(
diff --git a/cli/lsp/registries.rs b/cli/lsp/registries.rs
index 81e2552c0..c8e5dad60 100644
--- a/cli/lsp/registries.rs
+++ b/cli/lsp/registries.rs
@@ -30,7 +30,7 @@ use deno_core::url::Url;
 use deno_core::ModuleSpecifier;
 use deno_graph::Dependency;
 use deno_runtime::deno_web::BlobStore;
-use deno_runtime::permissions::Permissions;
+use deno_runtime::permissions::PermissionsContainer;
 use log::error;
 use once_cell::sync::Lazy;
 use regex::Regex;
@@ -519,7 +519,7 @@ impl ModuleRegistry {
       .file_fetcher
       .fetch_with_accept(
         specifier,
-        &mut Permissions::allow_all(),
+        PermissionsContainer::allow_all(),
         Some("application/vnd.deno.reg.v2+json, application/vnd.deno.reg.v1+json;q=0.9, application/json;q=0.8"),
       )
       .await;
@@ -617,7 +617,7 @@ impl ModuleRegistry {
         .ok()?;
         let file = self
           .file_fetcher
-          .fetch(&endpoint, &mut Permissions::allow_all())
+          .fetch(&endpoint, PermissionsContainer::allow_all())
           .await
           .ok()?;
         let documentation: lsp::Documentation =
@@ -973,7 +973,7 @@ impl ModuleRegistry {
     let specifier = Url::parse(url).ok()?;
     let file = self
       .file_fetcher
-      .fetch(&specifier, &mut Permissions::allow_all())
+      .fetch(&specifier, PermissionsContainer::allow_all())
       .await
       .ok()?;
     serde_json::from_str(&file.source).ok()
@@ -1030,7 +1030,7 @@ impl ModuleRegistry {
     let specifier = ModuleSpecifier::parse(url).ok()?;
     let file = self
       .file_fetcher
-      .fetch(&specifier, &mut Permissions::allow_all())
+      .fetch(&specifier, PermissionsContainer::allow_all())
       .await
       .map_err(|err| {
         error!(
@@ -1066,7 +1066,7 @@ impl ModuleRegistry {
         .ok()?;
     let file = self
       .file_fetcher
-      .fetch(&specifier, &mut Permissions::allow_all())
+      .fetch(&specifier, PermissionsContainer::allow_all())
       .await
       .map_err(|err| {
         error!(
diff --git a/cli/lsp/testing/execution.rs b/cli/lsp/testing/execution.rs
index 722f06e2c..a498df857 100644
--- a/cli/lsp/testing/execution.rs
+++ b/cli/lsp/testing/execution.rs
@@ -30,6 +30,7 @@ use deno_core::ModuleSpecifier;
 use deno_runtime::ops::io::Stdio;
 use deno_runtime::ops::io::StdioPipe;
 use deno_runtime::permissions::Permissions;
+use deno_runtime::permissions::PermissionsContainer;
 use deno_runtime::tokio_util::run_local;
 use indexmap::IndexMap;
 use std::collections::HashMap;
@@ -162,7 +163,7 @@ async fn test_specifier(
     let mut worker = create_main_worker_for_test_or_bench(
       &ps,
       specifier.clone(),
-      permissions,
+      PermissionsContainer::new(permissions),
       vec![ops::testing::init(sender, fail_fast_tracker, filter)],
       Stdio {
         stdin: StdioPipe::Inherit,
@@ -254,6 +255,9 @@ impl TestRun {
     lsp_log!("Executing test run with arguments: {}", args.join(" "));
     let flags = flags_from_vec(args.into_iter().map(String::from).collect())?;
     let ps = proc_state::ProcState::build(flags).await?;
+    // Various test files should not share the same permissions in terms of
+    // `PermissionsContainer` - otherwise granting/revoking permissions in one
+    // file would have impact on other files, which is undesirable.
     let permissions =
       Permissions::from_options(&ps.options.permissions_options())?;
     test::check_specifiers(
diff --git a/cli/module_loader.rs b/cli/module_loader.rs
index edc89be77..d452c30cf 100644
--- a/cli/module_loader.rs
+++ b/cli/module_loader.rs
@@ -21,7 +21,7 @@ use deno_core::ModuleSpecifier;
 use deno_core::ModuleType;
 use deno_core::OpState;
 use deno_core::SourceMapGetter;
-use deno_runtime::permissions::Permissions;
+use deno_runtime::permissions::PermissionsContainer;
 use std::cell::RefCell;
 use std::pin::Pin;
 use std::rc::Rc;
@@ -38,7 +38,7 @@ pub struct CliModuleLoader {
   /// The initial set of permissions used to resolve the static imports in the
   /// worker. They are decoupled from the worker (dynamic) permissions since
   /// read access errors must be raised based on the parent thread permissions.
-  pub root_permissions: Permissions,
+  pub root_permissions: PermissionsContainer,
   pub ps: ProcState,
 }
 
@@ -46,12 +46,15 @@ impl CliModuleLoader {
   pub fn new(ps: ProcState) -> Rc<Self> {
     Rc::new(CliModuleLoader {
       lib: ps.options.ts_type_lib_window(),
-      root_permissions: Permissions::allow_all(),
+      root_permissions: PermissionsContainer::allow_all(),
       ps,
     })
   }
 
-  pub fn new_for_worker(ps: ProcState, permissions: Permissions) -> Rc<Self> {
+  pub fn new_for_worker(
+    ps: ProcState,
+    permissions: PermissionsContainer,
+  ) -> Rc<Self> {
     Rc::new(CliModuleLoader {
       lib: ps.options.ts_type_lib_worker(),
       root_permissions: permissions,
@@ -235,7 +238,7 @@ impl ModuleLoader for CliModuleLoader {
     let ps = self.ps.clone();
     let state = op_state.borrow();
 
-    let dynamic_permissions = state.borrow::<Permissions>().clone();
+    let dynamic_permissions = state.borrow::<PermissionsContainer>().clone();
     let root_permissions = if is_dynamic {
       dynamic_permissions.clone()
     } else {
diff --git a/cli/ops/bench.rs b/cli/ops/bench.rs
index 6fc881f61..3b27ffa7e 100644
--- a/cli/ops/bench.rs
+++ b/cli/ops/bench.rs
@@ -9,7 +9,7 @@ use deno_core::ModuleSpecifier;
 use deno_core::OpState;
 use deno_runtime::permissions::create_child_permissions;
 use deno_runtime::permissions::ChildPermissionsArg;
-use deno_runtime::permissions::Permissions;
+use deno_runtime::permissions::PermissionsContainer;
 use serde::Deserialize;
 use serde::Serialize;
 use std::sync::atomic::AtomicUsize;
@@ -40,7 +40,7 @@ pub fn init(
 }
 
 #[derive(Clone)]
-struct PermissionsHolder(Uuid, Permissions);
+struct PermissionsHolder(Uuid, PermissionsContainer);
 
 #[op]
 pub fn op_pledge_test_permissions(
@@ -48,8 +48,12 @@ pub fn op_pledge_test_permissions(
   args: ChildPermissionsArg,
 ) -> Result<Uuid, AnyError> {
   let token = Uuid::new_v4();
-  let parent_permissions = state.borrow_mut::<Permissions>();
-  let worker_permissions = create_child_permissions(parent_permissions, args)?;
+  let parent_permissions = state.borrow_mut::<PermissionsContainer>();
+  let worker_permissions = {
+    let mut parent_permissions = parent_permissions.0.lock();
+    let perms = create_child_permissions(&mut parent_permissions, args)?;
+    PermissionsContainer::new(perms)
+  };
   let parent_permissions = parent_permissions.clone();
 
   if state.try_take::<PermissionsHolder>().is_some() {
@@ -59,7 +63,7 @@ pub fn op_pledge_test_permissions(
   state.put::<PermissionsHolder>(PermissionsHolder(token, parent_permissions));
 
   // NOTE: This call overrides current permission set for the worker
-  state.put::<Permissions>(worker_permissions);
+  state.put::<PermissionsContainer>(worker_permissions);
 
   Ok(token)
 }
@@ -75,7 +79,7 @@ pub fn op_restore_test_permissions(
     }
 
     let permissions = permissions_holder.1;
-    state.put::<Permissions>(permissions);
+    state.put::<PermissionsContainer>(permissions);
     Ok(())
   } else {
     Err(generic_error("no permissions to restore"))
diff --git a/cli/ops/testing.rs b/cli/ops/testing.rs
index b6fd29fc7..e5c0a2b99 100644
--- a/cli/ops/testing.rs
+++ b/cli/ops/testing.rs
@@ -17,7 +17,7 @@ use deno_core::ModuleSpecifier;
 use deno_core::OpState;
 use deno_runtime::permissions::create_child_permissions;
 use deno_runtime::permissions::ChildPermissionsArg;
-use deno_runtime::permissions::Permissions;
+use deno_runtime::permissions::PermissionsContainer;
 use serde::Deserialize;
 use serde::Deserializer;
 use serde::Serialize;
@@ -50,7 +50,7 @@ pub fn init(
 }
 
 #[derive(Clone)]
-struct PermissionsHolder(Uuid, Permissions);
+struct PermissionsHolder(Uuid, PermissionsContainer);
 
 #[op]
 pub fn op_pledge_test_permissions(
@@ -58,8 +58,12 @@ pub fn op_pledge_test_permissions(
   args: ChildPermissionsArg,
 ) -> Result<Uuid, AnyError> {
   let token = Uuid::new_v4();
-  let parent_permissions = state.borrow_mut::<Permissions>();
-  let worker_permissions = create_child_permissions(parent_permissions, args)?;
+  let parent_permissions = state.borrow_mut::<PermissionsContainer>();
+  let worker_permissions = {
+    let mut parent_permissions = parent_permissions.0.lock();
+    let perms = create_child_permissions(&mut parent_permissions, args)?;
+    PermissionsContainer::new(perms)
+  };
   let parent_permissions = parent_permissions.clone();
 
   if state.try_take::<PermissionsHolder>().is_some() {
@@ -68,7 +72,7 @@ pub fn op_pledge_test_permissions(
   state.put::<PermissionsHolder>(PermissionsHolder(token, parent_permissions));
 
   // NOTE: This call overrides current permission set for the worker
-  state.put::<Permissions>(worker_permissions);
+  state.put::<PermissionsContainer>(worker_permissions);
 
   Ok(token)
 }
@@ -84,7 +88,7 @@ pub fn op_restore_test_permissions(
     }
 
     let permissions = permissions_holder.1;
-    state.put::<Permissions>(permissions);
+    state.put::<PermissionsContainer>(permissions);
     Ok(())
   } else {
     Err(generic_error("no permissions to restore"))
diff --git a/cli/proc_state.rs b/cli/proc_state.rs
index eb672d8d0..0dd97b5e3 100644
--- a/cli/proc_state.rs
+++ b/cli/proc_state.rs
@@ -59,7 +59,7 @@ use deno_runtime::deno_node::NodeResolutionMode;
 use deno_runtime::deno_tls::rustls::RootCertStore;
 use deno_runtime::deno_web::BlobStore;
 use deno_runtime::inspector_server::InspectorServer;
-use deno_runtime::permissions::Permissions;
+use deno_runtime::permissions::PermissionsContainer;
 use import_map::ImportMap;
 use log::warn;
 use std::collections::HashSet;
@@ -181,7 +181,7 @@ impl ProcState {
     let maybe_import_map =
       if let Some(import_map_specifier) = maybe_import_map_specifier {
         let file = file_fetcher
-          .fetch(&import_map_specifier, &mut Permissions::allow_all())
+          .fetch(&import_map_specifier, PermissionsContainer::allow_all())
           .await
           .context(format!(
             "Unable to load '{}' import map",
@@ -289,8 +289,8 @@ impl ProcState {
     roots: Vec<ModuleSpecifier>,
     is_dynamic: bool,
     lib: TsTypeLib,
-    root_permissions: Permissions,
-    dynamic_permissions: Permissions,
+    root_permissions: PermissionsContainer,
+    dynamic_permissions: PermissionsContainer,
     reload_on_watch: bool,
   ) -> Result<(), AnyError> {
     log::debug!("Preparing module load.");
@@ -490,8 +490,8 @@ impl ProcState {
         specifiers,
         false,
         lib,
-        Permissions::allow_all(),
-        Permissions::allow_all(),
+        PermissionsContainer::allow_all(),
+        PermissionsContainer::allow_all(),
         false,
       )
       .await
@@ -668,8 +668,8 @@ impl ProcState {
     cache::FetchCacher::new(
       self.emit_cache.clone(),
       self.file_fetcher.clone(),
-      Permissions::allow_all(),
-      Permissions::allow_all(),
+      PermissionsContainer::allow_all(),
+      PermissionsContainer::allow_all(),
     )
   }
 
diff --git a/cli/standalone.rs b/cli/standalone.rs
index c93631327..2b0a77e18 100644
--- a/cli/standalone.rs
+++ b/cli/standalone.rs
@@ -29,6 +29,7 @@ use deno_runtime::deno_tls::rustls_pemfile;
 use deno_runtime::deno_web::BlobStore;
 use deno_runtime::fmt_errors::format_js_error;
 use deno_runtime::permissions::Permissions;
+use deno_runtime::permissions::PermissionsContainer;
 use deno_runtime::permissions::PermissionsOptions;
 use deno_runtime::worker::MainWorker;
 use deno_runtime::worker::WorkerOptions;
@@ -226,7 +227,9 @@ pub async fn run(
   let flags = metadata_to_flags(&metadata);
   let main_module = &metadata.entrypoint;
   let ps = ProcState::build(flags).await?;
-  let permissions = Permissions::from_options(&metadata.permissions)?;
+  let permissions = PermissionsContainer::new(Permissions::from_options(
+    &metadata.permissions,
+  )?);
   let blob_store = BlobStore::default();
   let broadcast_channel = InMemoryBroadcastChannel::default();
   let module_loader = Rc::new(EmbeddedModuleLoader {
diff --git a/cli/tests/run_tests.rs b/cli/tests/run_tests.rs
index dfe95d9a8..8460d3f8f 100644
--- a/cli/tests/run_tests.rs
+++ b/cli/tests/run_tests.rs
@@ -3725,4 +3725,21 @@ console.log("finish");
     args: "run --quiet run/001_hello.js --allow-net",
     output: "run/001_hello.js.out",
   });
+
+  // Regression test for https://github.com/denoland/deno/issues/16772
+  #[test]
+  fn file_fetcher_preserves_permissions() {
+    let _guard = util::http_server();
+    util::with_pty(&["repl"], |mut console| {
+      console.write_text(
+        "const a = import('http://127.0.0.1:4545/run/019_media_types.ts');",
+      );
+      console.write_text("y");
+      console.write_line("");
+      console.write_line("close();");
+      let output = console.read_all_output();
+      assert_contains!(output, "success");
+      assert_contains!(output, "true");
+    });
+  }
 }
diff --git a/cli/tools/bench.rs b/cli/tools/bench.rs
index 24fb07919..2d54b260d 100644
--- a/cli/tools/bench.rs
+++ b/cli/tools/bench.rs
@@ -28,6 +28,7 @@ use deno_core::futures::StreamExt;
 use deno_core::ModuleSpecifier;
 use deno_graph::ModuleKind;
 use deno_runtime::permissions::Permissions;
+use deno_runtime::permissions::PermissionsContainer;
 use deno_runtime::tokio_util::run_local;
 use indexmap::IndexMap;
 use log::Level;
@@ -337,8 +338,8 @@ async fn check_specifiers(
     specifiers,
     false,
     lib,
-    Permissions::allow_all(),
-    permissions,
+    PermissionsContainer::allow_all(),
+    PermissionsContainer::new(permissions),
     true,
   )
   .await?;
@@ -358,7 +359,7 @@ async fn bench_specifier(
   let mut worker = create_main_worker_for_test_or_bench(
     &ps,
     specifier.clone(),
-    permissions,
+    PermissionsContainer::new(permissions),
     vec![ops::bench::init(channel.clone(), filter)],
     Default::default(),
   )
@@ -490,6 +491,9 @@ pub async fn run_benchmarks(
   bench_flags: BenchFlags,
 ) -> Result<(), AnyError> {
   let ps = ProcState::build(flags).await?;
+  // Various bench files should not share the same permissions in terms of
+  // `PermissionsContainer` - otherwise granting/revoking permissions in one
+  // file would have impact on other files, which is undesirable.
   let permissions =
     Permissions::from_options(&ps.options.permissions_options())?;
 
@@ -527,6 +531,9 @@ pub async fn run_benchmarks_with_watch(
   bench_flags: BenchFlags,
 ) -> Result<(), AnyError> {
   let ps = ProcState::build(flags).await?;
+  // Various bench files should not share the same permissions in terms of
+  // `PermissionsContainer` - otherwise granting/revoking permissions in one
+  // file would have impact on other files, which is undesirable.
   let permissions =
     Permissions::from_options(&ps.options.permissions_options())?;
 
diff --git a/cli/tools/repl/mod.rs b/cli/tools/repl/mod.rs
index fc03dee2f..00f10b7d6 100644
--- a/cli/tools/repl/mod.rs
+++ b/cli/tools/repl/mod.rs
@@ -8,6 +8,7 @@ use crate::worker::create_main_worker;
 use deno_core::error::AnyError;
 use deno_core::resolve_url_or_path;
 use deno_runtime::permissions::Permissions;
+use deno_runtime::permissions::PermissionsContainer;
 use rustyline::error::ReadlineError;
 
 mod cdp;
@@ -72,7 +73,7 @@ async fn read_eval_file(
 
   let file = ps
     .file_fetcher
-    .fetch(&specifier, &mut Permissions::allow_all())
+    .fetch(&specifier, PermissionsContainer::allow_all())
     .await?;
 
   Ok((*file.source).to_string())
@@ -84,7 +85,9 @@ pub async fn run(flags: Flags, repl_flags: ReplFlags) -> Result<i32, AnyError> {
   let mut worker = create_main_worker(
     &ps,
     main_module.clone(),
-    Permissions::from_options(&ps.options.permissions_options())?,
+    PermissionsContainer::new(Permissions::from_options(
+      &ps.options.permissions_options(),
+    )?),
   )
   .await?;
   worker.setup_repl().await?;
diff --git a/cli/tools/run.rs b/cli/tools/run.rs
index af982e483..3830affed 100644
--- a/cli/tools/run.rs
+++ b/cli/tools/run.rs
@@ -9,6 +9,7 @@ use deno_ast::ModuleSpecifier;
 use deno_core::error::AnyError;
 use deno_core::resolve_url_or_path;
 use deno_runtime::permissions::Permissions;
+use deno_runtime::permissions::PermissionsContainer;
 
 use crate::args::EvalFlags;
 use crate::args::Flags;
@@ -56,8 +57,9 @@ To grant permissions, set them before the script argument. For example:
   } else {
     resolve_url_or_path(&run_flags.script)?
   };
-  let permissions =
-    Permissions::from_options(&ps.options.permissions_options())?;
+  let permissions = PermissionsContainer::new(Permissions::from_options(
+    &ps.options.permissions_options(),
+  )?);
   let mut worker =
     create_main_worker(&ps, main_module.clone(), permissions).await?;
 
@@ -71,7 +73,9 @@ pub async fn run_from_stdin(flags: Flags) -> Result<i32, AnyError> {
   let mut worker = create_main_worker(
     &ps.clone(),
     main_module.clone(),
-    Permissions::from_options(&ps.options.permissions_options())?,
+    PermissionsContainer::new(Permissions::from_options(
+      &ps.options.permissions_options(),
+    )?),
   )
   .await?;
 
@@ -110,8 +114,9 @@ async fn run_with_watch(flags: Flags, script: String) -> Result<i32, AnyError> {
       let ps =
         ProcState::build_for_file_watcher((*flags).clone(), sender.clone())
           .await?;
-      let permissions =
-        Permissions::from_options(&ps.options.permissions_options())?;
+      let permissions = PermissionsContainer::new(Permissions::from_options(
+        &ps.options.permissions_options(),
+      )?);
       let worker =
         create_main_worker(&ps, main_module.clone(), permissions).await?;
       worker.run_for_watcher().await?;
@@ -143,8 +148,9 @@ pub async fn eval_command(
   let main_module =
     resolve_url_or_path(&format!("./$deno$eval.{}", eval_flags.ext))?;
   let ps = ProcState::build(flags).await?;
-  let permissions =
-    Permissions::from_options(&ps.options.permissions_options())?;
+  let permissions = PermissionsContainer::new(Permissions::from_options(
+    &ps.options.permissions_options(),
+  )?);
   let mut worker =
     create_main_worker(&ps, main_module.clone(), permissions).await?;
   // Create a dummy source file.
diff --git a/cli/tools/standalone.rs b/cli/tools/standalone.rs
index 471c9605d..07baecc05 100644
--- a/cli/tools/standalone.rs
+++ b/cli/tools/standalone.rs
@@ -21,7 +21,7 @@ use deno_core::serde_json;
 use deno_core::url::Url;
 use deno_graph::ModuleSpecifier;
 use deno_runtime::colors;
-use deno_runtime::permissions::Permissions;
+use deno_runtime::permissions::PermissionsContainer;
 use std::env;
 use std::fs;
 use std::fs::File;
@@ -170,7 +170,7 @@ async fn create_standalone_binary(
       Some(import_map_specifier) => {
         let file = ps
           .file_fetcher
-          .fetch(&import_map_specifier, &mut Permissions::allow_all())
+          .fetch(&import_map_specifier, PermissionsContainer::allow_all())
           .await
           .context(format!(
             "Unable to load '{}' import map",
diff --git a/cli/tools/test.rs b/cli/tools/test.rs
index 35c0ea079..9d1774fff 100644
--- a/cli/tools/test.rs
+++ b/cli/tools/test.rs
@@ -37,6 +37,7 @@ use deno_runtime::fmt_errors::format_js_error;
 use deno_runtime::ops::io::Stdio;
 use deno_runtime::ops::io::StdioPipe;
 use deno_runtime::permissions::Permissions;
+use deno_runtime::permissions::PermissionsContainer;
 use deno_runtime::tokio_util::run_local;
 use indexmap::IndexMap;
 use log::Level;
@@ -723,7 +724,7 @@ async fn test_specifier(
   let mut worker = create_main_worker_for_test_or_bench(
     &ps,
     specifier.clone(),
-    permissions,
+    PermissionsContainer::new(permissions),
     vec![ops::testing::init(
       sender,
       fail_fast_tracker,
@@ -895,11 +896,8 @@ async fn fetch_inline_files(
 ) -> Result<Vec<File>, AnyError> {
   let mut files = Vec::new();
   for specifier in specifiers {
-    let mut fetch_permissions = Permissions::allow_all();
-    let file = ps
-      .file_fetcher
-      .fetch(&specifier, &mut fetch_permissions)
-      .await?;
+    let fetch_permissions = PermissionsContainer::allow_all();
+    let file = ps.file_fetcher.fetch(&specifier, fetch_permissions).await?;
 
     let inline_files = if file.media_type == MediaType::Unknown {
       extract_files_from_fenced_blocks(
@@ -957,8 +955,8 @@ pub async fn check_specifiers(
       specifiers,
       false,
       lib,
-      Permissions::allow_all(),
-      permissions.clone(),
+      PermissionsContainer::new(Permissions::allow_all()),
+      PermissionsContainer::new(permissions.clone()),
       false,
     )
     .await?;
@@ -979,8 +977,8 @@ pub async fn check_specifiers(
     module_specifiers,
     false,
     lib,
-    Permissions::allow_all(),
-    permissions,
+    PermissionsContainer::allow_all(),
+    PermissionsContainer::new(permissions),
     true,
   )
   .await?;
@@ -1324,7 +1322,7 @@ async fn fetch_specifiers_with_test_mode(
   for (specifier, mode) in &mut specifiers_with_mode {
     let file = ps
       .file_fetcher
-      .fetch(specifier, &mut Permissions::allow_all())
+      .fetch(specifier, PermissionsContainer::allow_all())
       .await?;
 
     if file.media_type == MediaType::Unknown
@@ -1342,6 +1340,9 @@ pub async fn run_tests(
   test_flags: TestFlags,
 ) -> Result<(), AnyError> {
   let ps = ProcState::build(flags).await?;
+  // Various test files should not share the same permissions in terms of
+  // `PermissionsContainer` - otherwise granting/revoking permissions in one
+  // file would have impact on other files, which is undesirable.
   let permissions =
     Permissions::from_options(&ps.options.permissions_options())?;
   let specifiers_with_mode = fetch_specifiers_with_test_mode(
@@ -1383,6 +1384,9 @@ pub async fn run_tests_with_watch(
   test_flags: TestFlags,
 ) -> Result<(), AnyError> {
   let ps = ProcState::build(flags).await?;
+  // Various test files should not share the same permissions in terms of
+  // `PermissionsContainer` - otherwise granting/revoking permissions in one
+  // file would have impact on other files, which is undesirable.
   let permissions =
     Permissions::from_options(&ps.options.permissions_options())?;
 
diff --git a/cli/worker.rs b/cli/worker.rs
index ea50966f4..2d29a7a53 100644
--- a/cli/worker.rs
+++ b/cli/worker.rs
@@ -16,7 +16,7 @@ use deno_runtime::colors;
 use deno_runtime::fmt_errors::format_js_error;
 use deno_runtime::ops::worker_host::CreateWebWorkerCb;
 use deno_runtime::ops::worker_host::WorkerEventCb;
-use deno_runtime::permissions::Permissions;
+use deno_runtime::permissions::PermissionsContainer;
 use deno_runtime::web_worker::WebWorker;
 use deno_runtime::web_worker::WebWorkerOptions;
 use deno_runtime::worker::MainWorker;
@@ -410,7 +410,7 @@ impl CliMainWorker {
 pub async fn create_main_worker(
   ps: &ProcState,
   main_module: ModuleSpecifier,
-  permissions: Permissions,
+  permissions: PermissionsContainer,
 ) -> Result<CliMainWorker, AnyError> {
   create_main_worker_internal(
     ps,
@@ -426,7 +426,7 @@ pub async fn create_main_worker(
 pub async fn create_main_worker_for_test_or_bench(
   ps: &ProcState,
   main_module: ModuleSpecifier,
-  permissions: Permissions,
+  permissions: PermissionsContainer,
   custom_extensions: Vec<Extension>,
   stdio: deno_runtime::ops::io::Stdio,
 ) -> Result<CliMainWorker, AnyError> {
@@ -444,7 +444,7 @@ pub async fn create_main_worker_for_test_or_bench(
 async fn create_main_worker_internal(
   ps: &ProcState,
   main_module: ModuleSpecifier,
-  permissions: Permissions,
+  permissions: PermissionsContainer,
   mut custom_extensions: Vec<Extension>,
   stdio: deno_runtime::ops::io::Stdio,
   bench_or_test: bool,
@@ -731,10 +731,11 @@ mod tests {
   use deno_core::{resolve_url_or_path, FsModuleLoader};
   use deno_runtime::deno_broadcast_channel::InMemoryBroadcastChannel;
   use deno_runtime::deno_web::BlobStore;
+  use deno_runtime::permissions::Permissions;
 
   fn create_test_worker() -> MainWorker {
     let main_module = resolve_url_or_path("./hello.js").unwrap();
-    let permissions = Permissions::default();
+    let permissions = PermissionsContainer::new(Permissions::default());
 
     let options = WorkerOptions {
       bootstrap: BootstrapOptions {