diff --git a/cli/args/flags.rs b/cli/args/flags.rs
index 257bf817857842..5ea8b8ecf3866c 100644
--- a/cli/args/flags.rs
+++ b/cli/args/flags.rs
@@ -1,7 +1,16 @@
 // Copyright 2018-2024 the Deno authors. All rights reserved. MIT license.
 
-use crate::args::resolve_no_prompt;
-use crate::util::fs::canonicalize_path;
+use std::collections::HashSet;
+use std::env;
+use std::ffi::OsString;
+use std::net::SocketAddr;
+use std::num::NonZeroU32;
+use std::num::NonZeroU8;
+use std::num::NonZeroUsize;
+use std::path::Path;
+use std::path::PathBuf;
+use std::str::FromStr;
+
 use clap::builder::styling::AnsiColor;
 use clap::builder::FalseyValueParser;
 use clap::error::ErrorKind;
@@ -23,22 +32,16 @@ use deno_core::normalize_path;
 use deno_core::resolve_url_or_path;
 use deno_core::url::Url;
 use deno_graph::GraphKind;
+use deno_runtime::colors;
 use deno_runtime::deno_permissions::parse_sys_kind;
 use deno_runtime::deno_permissions::PermissionsOptions;
 use log::debug;
 use log::Level;
 use serde::Deserialize;
 use serde::Serialize;
-use std::collections::HashSet;
-use std::env;
-use std::ffi::OsString;
-use std::net::SocketAddr;
-use std::num::NonZeroU32;
-use std::num::NonZeroU8;
-use std::num::NonZeroUsize;
-use std::path::Path;
-use std::path::PathBuf;
-use std::str::FromStr;
+
+use crate::args::resolve_no_prompt;
+use crate::util::fs::canonicalize_path;
 
 use super::flags_net;
 
@@ -681,6 +684,54 @@ impl PermissionFlags {
       Ok(Some(new_paths))
     }
 
+    fn resolve_allow_run(
+      allow_run: &[String],
+    ) -> Result<Vec<PathBuf>, AnyError> {
+      let mut new_allow_run = Vec::with_capacity(allow_run.len());
+      for command_name in allow_run {
+        if command_name.is_empty() {
+          bail!("Empty command name not allowed in --allow-run=...")
+        }
+        let command_path_result = which::which(command_name);
+        match command_path_result {
+          Ok(command_path) => new_allow_run.push(command_path),
+          Err(err) => {
+            log::info!(
+              "{} Failed to resolve '{}' for allow-run: {}",
+              colors::gray("Info"),
+              command_name,
+              err
+            );
+          }
+        }
+      }
+      Ok(new_allow_run)
+    }
+
+    let mut deny_write =
+      convert_option_str_to_path_buf(&self.deny_write, initial_cwd)?;
+    let allow_run = self
+      .allow_run
+      .as_ref()
+      .and_then(|raw_allow_run| match resolve_allow_run(raw_allow_run) {
+        Ok(resolved_allow_run) => {
+          if resolved_allow_run.is_empty() && !raw_allow_run.is_empty() {
+            None // convert to no permissions if now empty
+          } else {
+            Some(Ok(resolved_allow_run))
+          }
+        }
+        Err(err) => Some(Err(err)),
+      })
+      .transpose()?;
+    // add the allow_run list to deno_write
+    if let Some(allow_run_vec) = &allow_run {
+      if !allow_run_vec.is_empty() {
+        let deno_write = deny_write.get_or_insert_with(Vec::new);
+        deno_write.extend(allow_run_vec.iter().cloned());
+      }
+    }
+
     Ok(PermissionsOptions {
       allow_all: self.allow_all,
       allow_env: self.allow_env.clone(),
@@ -694,7 +745,7 @@ impl PermissionFlags {
         initial_cwd,
       )?,
       deny_read: convert_option_str_to_path_buf(&self.deny_read, initial_cwd)?,
-      allow_run: self.allow_run.clone(),
+      allow_run,
       deny_run: self.deny_run.clone(),
       allow_sys: self.allow_sys.clone(),
       deny_sys: self.deny_sys.clone(),
@@ -702,10 +753,7 @@ impl PermissionFlags {
         &self.allow_write,
         initial_cwd,
       )?,
-      deny_write: convert_option_str_to_path_buf(
-        &self.deny_write,
-        initial_cwd,
-      )?,
+      deny_write,
       prompt: !resolve_no_prompt(self),
     })
   }
diff --git a/cli/task_runner.rs b/cli/task_runner.rs
index e8937590db8ace..ab7163bc93b720 100644
--- a/cli/task_runner.rs
+++ b/cli/task_runner.rs
@@ -213,8 +213,8 @@ impl ShellCommand for NodeGypCommand {
   ) -> LocalBoxFuture<'static, ExecuteResult> {
     // at the moment this shell command is just to give a warning if node-gyp is not found
     // in the future, we could try to run/install node-gyp for the user with deno
-    if which::which("node-gyp").is_err() {
-      log::warn!("{}: node-gyp was used in a script, but was not listed as a dependency. Either add it as a dependency or install it globally (e.g. `npm install -g node-gyp`)", crate::colors::yellow("warning"));
+    if context.state.resolve_command_path("node-gyp").is_err() {
+      log::warn!("{} node-gyp was used in a script, but was not listed as a dependency. Either add it as a dependency or install it globally (e.g. `npm install -g node-gyp`)", crate::colors::yellow("Warning"));
     }
     ExecutableCommand::new(
       "node-gyp".to_string(),
diff --git a/runtime/ops/process.rs b/runtime/ops/process.rs
index 11e4390513069b..eb53151ced2dee 100644
--- a/runtime/ops/process.rs
+++ b/runtime/ops/process.rs
@@ -21,6 +21,9 @@ use serde::Deserialize;
 use serde::Serialize;
 use std::borrow::Cow;
 use std::cell::RefCell;
+use std::collections::HashMap;
+use std::path::Path;
+use std::path::PathBuf;
 use std::process::ExitStatus;
 use std::rc::Rc;
 use tokio::process::Command;
@@ -228,63 +231,15 @@ fn create_command(
   mut args: SpawnArgs,
   api_name: &str,
 ) -> Result<CreateCommand, AnyError> {
-  fn get_requires_allow_all_env_var(args: &SpawnArgs) -> Option<Cow<str>> {
-    fn requires_allow_all(key: &str) -> bool {
-      let key = key.trim();
-      // we could be more targted here, but there are quite a lot of
-      // LD_* and DYLD_* env variables
-      key.starts_with("LD_") || key.starts_with("DYLD_")
-    }
-
-    /// Checks if the user set this env var to an empty
-    /// string in order to clear it.
-    fn args_has_empty_env_value(args: &SpawnArgs, key_name: &str) -> bool {
-      args
-        .env
-        .iter()
-        .find(|(k, _)| k == key_name)
-        .map(|(_, v)| v.trim().is_empty())
-        .unwrap_or(false)
-    }
-
-    if let Some((key, _)) = args
-      .env
-      .iter()
-      .find(|(k, v)| requires_allow_all(k) && !v.trim().is_empty())
-    {
-      return Some(key.into());
-    }
-
-    if !args.clear_env {
-      if let Some((key, _)) = std::env::vars().find(|(k, v)| {
-        requires_allow_all(k)
-          && !v.trim().is_empty()
-          && !args_has_empty_env_value(args, k)
-      }) {
-        return Some(key.into());
-      }
-    }
-
-    None
-  }
-
-  {
-    let permissions = state.borrow_mut::<PermissionsContainer>();
-    permissions.check_run(&args.cmd, api_name)?;
-    if permissions.check_run_all(api_name).is_err() {
-      // error the same on all platforms
-      if let Some(name) = get_requires_allow_all_env_var(&args) {
-        // we don't allow users to launch subprocesses with any LD_ or DYLD_*
-        // env vars set because this allows executing code (ex. LD_PRELOAD)
-        return Err(deno_core::error::custom_error(
-          "PermissionDenied",
-          format!("Requires --allow-all permissions to spawn subprocess with {} environment variable.", name)
-        ));
-      }
-    }
-  }
-
-  let mut command = std::process::Command::new(args.cmd);
+  let (cmd, run_env) = compute_run_cmd_and_check_permissions(
+    &args.cmd,
+    args.cwd.as_deref(),
+    &args.env,
+    args.clear_env,
+    state,
+    api_name,
+  )?;
+  let mut command = std::process::Command::new(cmd);
 
   #[cfg(windows)]
   if args.windows_raw_arguments {
@@ -298,14 +253,9 @@ fn create_command(
   #[cfg(not(windows))]
   command.args(args.args);
 
-  if let Some(cwd) = args.cwd {
-    command.current_dir(cwd);
-  }
-
-  if args.clear_env {
-    command.env_clear();
-  }
-  command.envs(args.env);
+  command.current_dir(run_env.cwd);
+  command.env_clear();
+  command.envs(run_env.envs);
 
   #[cfg(unix)]
   if let Some(gid) = args.gid {
@@ -554,6 +504,133 @@ fn close_raw_handle(handle: deno_io::RawBiPipeHandle) {
   }
 }
 
+fn compute_run_cmd_and_check_permissions(
+  arg_cmd: &str,
+  arg_cwd: Option<&str>,
+  arg_envs: &[(String, String)],
+  arg_clear_env: bool,
+  state: &mut OpState,
+  api_name: &str,
+) -> Result<(PathBuf, RunEnv), AnyError> {
+  let run_env = compute_run_env(arg_cwd, arg_envs, arg_clear_env)
+    .with_context(|| format!("Failed to spawn '{}'", arg_cmd))?;
+  let cmd = resolve_cmd(arg_cmd, &run_env)
+    .with_context(|| format!("Failed to spawn '{}'", arg_cmd))?;
+  check_run_permission(state, &cmd, &run_env, api_name)?;
+  Ok((cmd, run_env))
+}
+
+struct RunEnv {
+  envs: HashMap<String, String>,
+  cwd: PathBuf,
+}
+
+/// Computes the current environment, which will then be used to inform
+/// permissions and finally spawning. This is very important to compute
+/// ahead of time so that the environment used to verify permissions is
+/// the same environment used to spawn the sub command. This protects against
+/// someone doing timing attacks by changing the environment on a worker.
+fn compute_run_env(
+  arg_cwd: Option<&str>,
+  arg_envs: &[(String, String)],
+  arg_clear_env: bool,
+) -> Result<RunEnv, AnyError> {
+  #[allow(clippy::disallowed_methods)]
+  let cwd = std::env::current_dir().context("failed resolving cwd")?;
+  let cwd = arg_cwd
+    .map(|cwd_arg| resolve_path(cwd_arg, &cwd))
+    .unwrap_or(cwd);
+  let envs = if arg_clear_env {
+    arg_envs.iter().cloned().collect()
+  } else {
+    let mut envs = std::env::vars().collect::<HashMap<_, _>>();
+    for (key, value) in arg_envs {
+      envs.insert(key.clone(), value.clone());
+    }
+    envs
+  };
+  Ok(RunEnv { envs, cwd })
+}
+
+fn resolve_cmd(cmd: &str, env: &RunEnv) -> Result<PathBuf, AnyError> {
+  let is_path = cmd.contains('/');
+  #[cfg(windows)]
+  let is_path = is_path || cmd.contains('\\') || Path::new(&cmd).is_absolute();
+  if is_path {
+    Ok(resolve_path(cmd, &env.cwd))
+  } else {
+    let path = env.envs.get("PATH").or_else(|| {
+      if cfg!(windows) {
+        env.envs.iter().find_map(|(k, v)| {
+          if k.to_uppercase() == "PATH" {
+            Some(v)
+          } else {
+            None
+          }
+        })
+      } else {
+        None
+      }
+    });
+    match which::which_in(cmd, path, &env.cwd) {
+      Ok(cmd) => Ok(cmd),
+      Err(which::Error::CannotFindBinaryPath) => {
+        Err(std::io::Error::from(std::io::ErrorKind::NotFound).into())
+      }
+      Err(err) => Err(err.into()),
+    }
+  }
+}
+
+fn resolve_path(path: &str, cwd: &Path) -> PathBuf {
+  deno_core::normalize_path(cwd.join(path))
+}
+
+fn check_run_permission(
+  state: &mut OpState,
+  cmd: &Path,
+  run_env: &RunEnv,
+  api_name: &str,
+) -> Result<(), AnyError> {
+  let permissions = state.borrow_mut::<PermissionsContainer>();
+  if !permissions.query_run_all(api_name) {
+    // error the same on all platforms
+    let env_var_names = get_requires_allow_all_env_vars(run_env);
+    if !env_var_names.is_empty() {
+      // we don't allow users to launch subprocesses with any LD_ or DYLD_*
+      // env vars set because this allows executing code (ex. LD_PRELOAD)
+      return Err(deno_core::error::custom_error(
+        "PermissionDenied",
+        format!(
+          "Requires --allow-all permissions to spawn subprocess with {} environment variable{}.",
+          env_var_names.join(", "),
+          if env_var_names.len() != 1 { "s" } else { "" }
+        )
+      ));
+    }
+    permissions.check_run(cmd, api_name)?;
+  }
+  Ok(())
+}
+
+fn get_requires_allow_all_env_vars(env: &RunEnv) -> Vec<&str> {
+  fn requires_allow_all(key: &str) -> bool {
+    let key = key.trim();
+    // we could be more targted here, but there are quite a lot of
+    // LD_* and DYLD_* env variables
+    key.starts_with("LD_") || key.starts_with("DYLD_")
+  }
+
+  let mut found_envs = env
+    .envs
+    .iter()
+    .filter(|(k, v)| requires_allow_all(k) && !v.trim().is_empty())
+    .map(|(k, _)| k.as_str())
+    .collect::<Vec<_>>();
+  found_envs.sort();
+  found_envs
+}
+
 #[op2]
 #[serde]
 fn op_spawn_child(
@@ -634,6 +711,8 @@ fn op_spawn_kill(
 }
 
 mod deprecated {
+  use deno_core::anyhow;
+
   use super::*;
 
   #[derive(Deserialize)]
@@ -681,20 +760,24 @@ mod deprecated {
     #[serde] run_args: RunArgs,
   ) -> Result<RunInfo, AnyError> {
     let args = run_args.cmd;
-    state
-      .borrow_mut::<PermissionsContainer>()
-      .check_run(&args[0], "Deno.run()")?;
-    let env = run_args.env;
-    let cwd = run_args.cwd;
-
-    let mut c = Command::new(args.first().unwrap());
-    (1..args.len()).for_each(|i| {
-      let arg = args.get(i).unwrap();
+    let cmd = args.first().ok_or_else(|| anyhow::anyhow!("Missing cmd"))?;
+    let (cmd, run_env) = compute_run_cmd_and_check_permissions(
+      cmd,
+      run_args.cwd.as_deref(),
+      &run_args.env,
+      /* clear env */ false,
+      state,
+      "Deno.run()",
+    )?;
+
+    let mut c = Command::new(cmd);
+    for arg in args.iter().skip(1) {
       c.arg(arg);
-    });
-    cwd.map(|d| c.current_dir(d));
+    }
+    c.current_dir(run_env.cwd);
 
-    for (key, value) in &env {
+    c.env_clear();
+    for (key, value) in run_env.envs {
       c.env(key, value);
     }
 
diff --git a/runtime/permissions/lib.rs b/runtime/permissions/lib.rs
index 7227bebf8c2349..2eacd8bcc41a5a 100644
--- a/runtime/permissions/lib.rs
+++ b/runtime/permissions/lib.rs
@@ -32,7 +32,6 @@ use std::path::PathBuf;
 use std::str::FromStr;
 use std::string::ToString;
 use std::sync::Arc;
-use which::which;
 
 pub mod prompter;
 use prompter::permission_prompt;
@@ -317,7 +316,7 @@ pub trait Descriptor: Eq + Clone + Hash {
 
   /// Parse this descriptor from a list of Self::Arg, which may have been converted from
   /// command-line strings.
-  fn parse(list: &Option<Vec<Self::Arg>>) -> Result<HashSet<Self>, AnyError>;
+  fn parse(list: Option<&[Self::Arg]>) -> Result<HashSet<Self>, AnyError>;
 
   /// Generic check function to check this descriptor against a `UnaryPermission`.
   fn check_in_permission(
@@ -333,9 +332,6 @@ pub trait Descriptor: Eq + Clone + Hash {
   fn stronger_than(&self, other: &Self) -> bool {
     self == other
   }
-  fn aliases(&self) -> Vec<Self> {
-    vec![]
-  }
 }
 
 #[derive(Clone, Debug, Eq, PartialEq)]
@@ -423,43 +419,33 @@ impl<T: Descriptor + Hash> UnaryPermission<T> {
     desc: Option<&T>,
     allow_partial: AllowPartial,
   ) -> PermissionState {
-    let aliases = desc.map_or(vec![], T::aliases);
-    for desc in [desc]
-      .into_iter()
-      .chain(aliases.iter().map(Some).collect::<Vec<_>>())
-    {
-      let state = if self.is_flag_denied(desc) || self.is_prompt_denied(desc) {
-        PermissionState::Denied
-      } else if self.is_granted(desc) {
-        match allow_partial {
-          AllowPartial::TreatAsGranted => PermissionState::Granted,
-          AllowPartial::TreatAsDenied => {
-            if self.is_partial_flag_denied(desc) {
-              PermissionState::Denied
-            } else {
-              PermissionState::Granted
-            }
+    if self.is_flag_denied(desc) || self.is_prompt_denied(desc) {
+      PermissionState::Denied
+    } else if self.is_granted(desc) {
+      match allow_partial {
+        AllowPartial::TreatAsGranted => PermissionState::Granted,
+        AllowPartial::TreatAsDenied => {
+          if self.is_partial_flag_denied(desc) {
+            PermissionState::Denied
+          } else {
+            PermissionState::Granted
           }
-          AllowPartial::TreatAsPartialGranted => {
-            if self.is_partial_flag_denied(desc) {
-              PermissionState::GrantedPartial
-            } else {
-              PermissionState::Granted
-            }
+        }
+        AllowPartial::TreatAsPartialGranted => {
+          if self.is_partial_flag_denied(desc) {
+            PermissionState::GrantedPartial
+          } else {
+            PermissionState::Granted
           }
         }
-      } else if matches!(allow_partial, AllowPartial::TreatAsDenied)
-        && self.is_partial_flag_denied(desc)
-      {
-        PermissionState::Denied
-      } else {
-        PermissionState::Prompt
-      };
-      if state != PermissionState::Prompt {
-        return state;
       }
+    } else if matches!(allow_partial, AllowPartial::TreatAsDenied)
+      && self.is_partial_flag_denied(desc)
+    {
+      PermissionState::Denied
+    } else {
+      PermissionState::Prompt
     }
-    PermissionState::Prompt
   }
 
   fn request_desc(
@@ -512,9 +498,6 @@ impl<T: Descriptor + Hash> UnaryPermission<T> {
     match desc {
       Some(desc) => {
         self.granted_list.retain(|v| !v.stronger_than(desc));
-        for alias in desc.aliases() {
-          self.granted_list.retain(|v| !v.stronger_than(&alias));
-        }
       }
       None => {
         self.granted_global = false;
@@ -582,11 +565,7 @@ impl<T: Descriptor + Hash> UnaryPermission<T> {
   ) {
     match desc {
       Some(desc) => {
-        let aliases = desc.aliases();
         list.insert(desc);
-        for alias in aliases {
-          list.insert(alias);
-        }
       }
       None => *list_global = true,
     }
@@ -612,7 +591,7 @@ impl<T: Descriptor + Hash> UnaryPermission<T> {
       ChildUnaryPermissionArg::GrantedList(granted_list) => {
         let granted: Vec<T::Arg> =
           granted_list.into_iter().map(From::from).collect();
-        perms.granted_list = T::parse(&Some(granted))?;
+        perms.granted_list = T::parse(Some(&granted))?;
         if !perms
           .granted_list
           .iter()
@@ -649,7 +628,7 @@ impl Descriptor for ReadDescriptor {
     perm.check_desc(Some(self), true, api_name, || None)
   }
 
-  fn parse(args: &Option<Vec<Self::Arg>>) -> Result<HashSet<Self>, AnyError> {
+  fn parse(args: Option<&[Self::Arg]>) -> Result<HashSet<Self>, AnyError> {
     parse_path_list(args, ReadDescriptor)
   }
 
@@ -681,7 +660,7 @@ impl Descriptor for WriteDescriptor {
     perm.check_desc(Some(self), true, api_name, || None)
   }
 
-  fn parse(args: &Option<Vec<Self::Arg>>) -> Result<HashSet<Self>, AnyError> {
+  fn parse(args: Option<&[Self::Arg]>) -> Result<HashSet<Self>, AnyError> {
     parse_path_list(args, WriteDescriptor)
   }
 
@@ -754,7 +733,7 @@ impl Descriptor for NetDescriptor {
     perm.check_desc(Some(self), false, api_name, || None)
   }
 
-  fn parse(args: &Option<Vec<Self::Arg>>) -> Result<HashSet<Self>, AnyError> {
+  fn parse(args: Option<&[Self::Arg]>) -> Result<HashSet<Self>, AnyError> {
     parse_net_list(args)
   }
 
@@ -864,7 +843,7 @@ impl Descriptor for EnvDescriptor {
     perm.check_desc(Some(self), false, api_name, || None)
   }
 
-  fn parse(list: &Option<Vec<Self::Arg>>) -> Result<HashSet<Self>, AnyError> {
+  fn parse(list: Option<&[Self::Arg]>) -> Result<HashSet<Self>, AnyError> {
     parse_env_list(list)
   }
 
@@ -883,6 +862,11 @@ impl AsRef<str> for EnvDescriptor {
   }
 }
 
+pub enum RunDescriptorArg {
+  Name(String),
+  Path(PathBuf),
+}
+
 #[derive(Clone, Eq, PartialEq, Hash, Debug)]
 pub enum RunDescriptor {
   /// Warning: You may want to construct with `RunDescriptor::from()` for case
@@ -893,8 +877,26 @@ pub enum RunDescriptor {
   Path(PathBuf),
 }
 
+impl From<String> for RunDescriptorArg {
+  fn from(s: String) -> Self {
+    #[cfg(windows)]
+    let s = s.to_lowercase();
+    let is_path = s.contains('/');
+    #[cfg(windows)]
+    let is_path = is_path || s.contains('\\') || Path::new(&s).is_absolute();
+    if is_path {
+      Self::Path(resolve_from_cwd(Path::new(&s)).unwrap())
+    } else {
+      match which::which(&s) {
+        Ok(path) => Self::Path(path),
+        Err(_) => Self::Name(s),
+      }
+    }
+  }
+}
+
 impl Descriptor for RunDescriptor {
-  type Arg = String;
+  type Arg = RunDescriptorArg;
 
   fn check_in_permission(
     &self,
@@ -905,7 +907,7 @@ impl Descriptor for RunDescriptor {
     perm.check_desc(Some(self), false, api_name, || None)
   }
 
-  fn parse(args: &Option<Vec<Self::Arg>>) -> Result<HashSet<Self>, AnyError> {
+  fn parse(args: Option<&[Self::Arg]>) -> Result<HashSet<Self>, AnyError> {
     parse_run_list(args)
   }
 
@@ -916,16 +918,6 @@ impl Descriptor for RunDescriptor {
   fn name(&self) -> Cow<str> {
     Cow::from(self.to_string())
   }
-
-  fn aliases(&self) -> Vec<Self> {
-    match self {
-      RunDescriptor::Name(name) => match which(name) {
-        Ok(path) => vec![RunDescriptor::Path(path)],
-        Err(_) => vec![],
-      },
-      RunDescriptor::Path(_) => vec![],
-    }
-  }
 }
 
 impl From<String> for RunDescriptor {
@@ -938,7 +930,10 @@ impl From<String> for RunDescriptor {
     if is_path {
       Self::Path(resolve_from_cwd(Path::new(&s)).unwrap())
     } else {
-      Self::Name(s)
+      match which::which(&s) {
+        Ok(path) => Self::Path(path),
+        Err(_) => Self::Name(s),
+      }
     }
   }
 }
@@ -947,11 +942,7 @@ impl From<PathBuf> for RunDescriptor {
   fn from(p: PathBuf) -> Self {
     #[cfg(windows)]
     let p = PathBuf::from(p.to_string_lossy().to_string().to_lowercase());
-    if p.is_absolute() {
-      Self::Path(p)
-    } else {
-      Self::Path(resolve_from_cwd(&p).unwrap())
-    }
+    Self::Path(resolve_from_cwd(&p).unwrap())
   }
 }
 
@@ -988,7 +979,7 @@ impl Descriptor for SysDescriptor {
     perm.check_desc(Some(self), false, api_name, || None)
   }
 
-  fn parse(list: &Option<Vec<Self::Arg>>) -> Result<HashSet<Self>, AnyError> {
+  fn parse(list: Option<&[Self::Arg]>) -> Result<HashSet<Self>, AnyError> {
     parse_sys_list(list)
   }
 
@@ -1025,7 +1016,7 @@ impl Descriptor for FfiDescriptor {
     perm.check_desc(Some(self), true, api_name, || None)
   }
 
-  fn parse(list: &Option<Vec<Self::Arg>>) -> Result<HashSet<Self>, AnyError> {
+  fn parse(list: Option<&[Self::Arg]>) -> Result<HashSet<Self>, AnyError> {
     parse_path_list(list, FfiDescriptor)
   }
 
@@ -1330,15 +1321,16 @@ impl UnaryPermission<RunDescriptor> {
 
   pub fn check(
     &mut self,
-    cmd: &str,
+    cmd: &Path,
     api_name: Option<&str>,
   ) -> Result<(), AnyError> {
+    debug_assert!(cmd.is_absolute());
     skip_check_if_is_permission_fully_granted!(self);
     self.check_desc(
-      Some(&RunDescriptor::from(cmd.to_string())),
+      Some(&RunDescriptor::Path(cmd.to_path_buf())),
       false,
       api_name,
-      || Some(format!("\"{}\"", cmd)),
+      || Some(format!("\"{}\"", cmd.display())),
     )
   }
 
@@ -1346,6 +1338,21 @@ impl UnaryPermission<RunDescriptor> {
     skip_check_if_is_permission_fully_granted!(self);
     self.check_desc(None, false, api_name, || None)
   }
+
+  /// Queries without prompting
+  pub fn query_all(&mut self, api_name: Option<&str>) -> bool {
+    if self.is_allow_all() {
+      return true;
+    }
+    let (result, _prompted, _is_allow_all) =
+      self.query_desc(None, AllowPartial::TreatAsDenied).check2(
+        RunDescriptor::flag_name(),
+        api_name,
+        || None,
+        /* prompt */ false,
+      );
+    result.is_ok()
+  }
 }
 
 impl UnaryPermission<FfiDescriptor> {
@@ -1429,7 +1436,7 @@ pub struct PermissionsOptions {
   pub deny_ffi: Option<Vec<PathBuf>>,
   pub allow_read: Option<Vec<PathBuf>>,
   pub deny_read: Option<Vec<PathBuf>>,
-  pub allow_run: Option<Vec<String>>,
+  pub allow_run: Option<Vec<PathBuf>>,
   pub deny_run: Option<Vec<String>>,
   pub allow_sys: Option<Vec<String>>,
   pub deny_sys: Option<Vec<String>>,
@@ -1440,8 +1447,8 @@ pub struct PermissionsOptions {
 
 impl Permissions {
   pub fn new_unary<T>(
-    allow_list: &Option<Vec<T::Arg>>,
-    deny_list: &Option<Vec<T::Arg>>,
+    allow_list: Option<&[T::Arg]>,
+    deny_list: Option<&[T::Arg]>,
     prompt: bool,
   ) -> Result<UnaryPermission<T>, AnyError>
   where
@@ -1470,38 +1477,54 @@ impl Permissions {
   pub fn from_options(opts: &PermissionsOptions) -> Result<Self, AnyError> {
     Ok(Self {
       read: Permissions::new_unary(
-        &opts.allow_read,
-        &opts.deny_read,
+        opts.allow_read.as_deref(),
+        opts.deny_read.as_deref(),
         opts.prompt,
       )?,
       write: Permissions::new_unary(
-        &opts.allow_write,
-        &opts.deny_write,
+        opts.allow_write.as_deref(),
+        opts.deny_write.as_deref(),
         opts.prompt,
       )?,
       net: Permissions::new_unary(
-        &opts.allow_net,
-        &opts.deny_net,
+        opts.allow_net.as_deref(),
+        opts.deny_net.as_deref(),
         opts.prompt,
       )?,
       env: Permissions::new_unary(
-        &opts.allow_env,
-        &opts.deny_env,
+        opts.allow_env.as_deref(),
+        opts.deny_env.as_deref(),
         opts.prompt,
       )?,
       sys: Permissions::new_unary(
-        &opts.allow_sys,
-        &opts.deny_sys,
+        opts.allow_sys.as_deref(),
+        opts.deny_sys.as_deref(),
         opts.prompt,
       )?,
       run: Permissions::new_unary(
-        &opts.allow_run,
-        &opts.deny_run,
+        opts
+          .allow_run
+          .as_ref()
+          .map(|d| {
+            d.iter()
+              .map(|s| RunDescriptorArg::Path(s.clone()))
+              .collect::<Vec<_>>()
+          })
+          .as_deref(),
+        opts
+          .deny_run
+          .as_ref()
+          .map(|d| {
+            d.iter()
+              .map(|s| RunDescriptorArg::from(s.clone()))
+              .collect::<Vec<_>>()
+          })
+          .as_deref(),
         opts.prompt,
       )?,
       ffi: Permissions::new_unary(
-        &opts.allow_ffi,
-        &opts.deny_ffi,
+        opts.allow_ffi.as_deref(),
+        opts.deny_ffi.as_deref(),
         opts.prompt,
       )?,
       all: Permissions::new_all(opts.allow_all),
@@ -1534,13 +1557,13 @@ impl Permissions {
 
   fn none(prompt: bool) -> Self {
     Self {
-      read: Permissions::new_unary(&None, &None, prompt).unwrap(),
-      write: Permissions::new_unary(&None, &None, prompt).unwrap(),
-      net: Permissions::new_unary(&None, &None, prompt).unwrap(),
-      env: Permissions::new_unary(&None, &None, prompt).unwrap(),
-      sys: Permissions::new_unary(&None, &None, prompt).unwrap(),
-      run: Permissions::new_unary(&None, &None, prompt).unwrap(),
-      ffi: Permissions::new_unary(&None, &None, prompt).unwrap(),
+      read: Permissions::new_unary(None, None, prompt).unwrap(),
+      write: Permissions::new_unary(None, None, prompt).unwrap(),
+      net: Permissions::new_unary(None, None, prompt).unwrap(),
+      env: Permissions::new_unary(None, None, prompt).unwrap(),
+      sys: Permissions::new_unary(None, None, prompt).unwrap(),
+      run: Permissions::new_unary(None, None, prompt).unwrap(),
+      ffi: Permissions::new_unary(None, None, prompt).unwrap(),
       all: Permissions::new_all(false),
     }
   }
@@ -1669,7 +1692,7 @@ impl PermissionsContainer {
   #[inline(always)]
   pub fn check_run(
     &mut self,
-    cmd: &str,
+    cmd: &Path,
     api_name: &str,
   ) -> Result<(), AnyError> {
     self.0.lock().run.check(cmd, Some(api_name))
@@ -1680,6 +1703,11 @@ impl PermissionsContainer {
     self.0.lock().run.check_all(Some(api_name))
   }
 
+  #[inline(always)]
+  pub fn query_run_all(&mut self, api_name: &str) -> bool {
+    self.0.lock().run.query_all(Some(api_name))
+  }
+
   #[inline(always)]
   pub fn check_sys(&self, kind: &str, api_name: &str) -> Result<(), AnyError> {
     self.0.lock().sys.check(kind, Some(api_name))
@@ -1871,12 +1899,12 @@ const fn unit_permission_from_flag_bools(
   }
 }
 
-fn global_from_option<T>(flag: &Option<Vec<T>>) -> bool {
+fn global_from_option<T>(flag: Option<&[T]>) -> bool {
   matches!(flag, Some(v) if v.is_empty())
 }
 
 fn parse_net_list(
-  list: &Option<Vec<String>>,
+  list: Option<&[String]>,
 ) -> Result<HashSet<NetDescriptor>, AnyError> {
   if let Some(v) = list {
     v.iter()
@@ -1888,7 +1916,7 @@ fn parse_net_list(
 }
 
 fn parse_env_list(
-  list: &Option<Vec<String>>,
+  list: Option<&[String]>,
 ) -> Result<HashSet<EnvDescriptor>, AnyError> {
   if let Some(v) = list {
     v.iter()
@@ -1906,7 +1934,7 @@ fn parse_env_list(
 }
 
 fn parse_path_list<T: Descriptor + Hash>(
-  list: &Option<Vec<PathBuf>>,
+  list: Option<&[PathBuf]>,
   f: fn(PathBuf) -> T,
 ) -> Result<HashSet<T>, AnyError> {
   if let Some(v) = list {
@@ -1925,7 +1953,7 @@ fn parse_path_list<T: Descriptor + Hash>(
 }
 
 fn parse_sys_list(
-  list: &Option<Vec<String>>,
+  list: Option<&[String]>,
 ) -> Result<HashSet<SysDescriptor>, AnyError> {
   if let Some(v) = list {
     v.iter()
@@ -1943,22 +1971,19 @@ fn parse_sys_list(
 }
 
 fn parse_run_list(
-  list: &Option<Vec<String>>,
+  list: Option<&[RunDescriptorArg]>,
 ) -> Result<HashSet<RunDescriptor>, AnyError> {
-  let mut result = HashSet::new();
-  if let Some(v) = list {
-    for s in v {
-      if s.is_empty() {
-        return Err(AnyError::msg("Empty path is not allowed"));
-      } else {
-        let desc = RunDescriptor::from(s.to_string());
-        let aliases = desc.aliases();
-        result.insert(desc);
-        result.extend(aliases);
-      }
-    }
-  }
-  Ok(result)
+  let Some(v) = list else {
+    return Ok(HashSet::new());
+  };
+  Ok(
+    v.iter()
+      .map(|arg| match arg {
+        RunDescriptorArg::Name(s) => RunDescriptor::Name(s.clone()),
+        RunDescriptorArg::Path(l) => RunDescriptor::Path(l.clone()),
+      })
+      .collect(),
+  )
 }
 
 fn escalation_error() -> AnyError {
@@ -2298,6 +2323,9 @@ mod tests {
   macro_rules! svec {
       ($($x:expr),*) => (vec![$($x.to_string()),*]);
   }
+  macro_rules! sarr {
+      ($($x:expr),*) => ([$($x.to_string()),*]);
+  }
 
   #[test]
   fn check_paths() {
@@ -2678,94 +2706,88 @@ mod tests {
     set_prompter(Box::new(TestPrompter));
     let perms1 = Permissions::allow_all();
     let perms2 = Permissions {
-      read: Permissions::new_unary(
-        &Some(vec![PathBuf::from("/foo")]),
-        &None,
-        false,
-      )
-      .unwrap(),
+      read: Permissions::new_unary(Some(&[PathBuf::from("/foo")]), None, false)
+        .unwrap(),
       write: Permissions::new_unary(
-        &Some(vec![PathBuf::from("/foo")]),
-        &None,
+        Some(&[PathBuf::from("/foo")]),
+        None,
         false,
       )
       .unwrap(),
-      ffi: Permissions::new_unary(
-        &Some(vec![PathBuf::from("/foo")]),
-        &None,
+      ffi: Permissions::new_unary(Some(&[PathBuf::from("/foo")]), None, false)
+        .unwrap(),
+      net: Permissions::new_unary(Some(&sarr!["127.0.0.1:8000"]), None, false)
+        .unwrap(),
+      env: Permissions::new_unary(Some(&sarr!["HOME"]), None, false).unwrap(),
+      sys: Permissions::new_unary(Some(&sarr!["hostname"]), None, false)
+        .unwrap(),
+      run: Permissions::new_unary(
+        Some(&["deno".to_string().into()]),
+        None,
         false,
       )
       .unwrap(),
-      net: Permissions::new_unary(&Some(svec!["127.0.0.1:8000"]), &None, false)
-        .unwrap(),
-      env: Permissions::new_unary(&Some(svec!["HOME"]), &None, false).unwrap(),
-      sys: Permissions::new_unary(&Some(svec!["hostname"]), &None, false)
-        .unwrap(),
-      run: Permissions::new_unary(&Some(svec!["deno"]), &None, false).unwrap(),
       all: Permissions::new_all(false),
     };
     let perms3 = Permissions {
-      read: Permissions::new_unary(
-        &None,
-        &Some(vec![PathBuf::from("/foo")]),
-        false,
-      )
-      .unwrap(),
+      read: Permissions::new_unary(None, Some(&[PathBuf::from("/foo")]), false)
+        .unwrap(),
       write: Permissions::new_unary(
-        &None,
-        &Some(vec![PathBuf::from("/foo")]),
+        None,
+        Some(&[PathBuf::from("/foo")]),
         false,
       )
       .unwrap(),
-      ffi: Permissions::new_unary(
-        &None,
-        &Some(vec![PathBuf::from("/foo")]),
+      ffi: Permissions::new_unary(None, Some(&[PathBuf::from("/foo")]), false)
+        .unwrap(),
+      net: Permissions::new_unary(None, Some(&sarr!["127.0.0.1:8000"]), false)
+        .unwrap(),
+      env: Permissions::new_unary(None, Some(&sarr!["HOME"]), false).unwrap(),
+      sys: Permissions::new_unary(None, Some(&sarr!["hostname"]), false)
+        .unwrap(),
+      run: Permissions::new_unary(
+        None,
+        Some(&["deno".to_string().into()]),
         false,
       )
       .unwrap(),
-      net: Permissions::new_unary(&None, &Some(svec!["127.0.0.1:8000"]), false)
-        .unwrap(),
-      env: Permissions::new_unary(&None, &Some(svec!["HOME"]), false).unwrap(),
-      sys: Permissions::new_unary(&None, &Some(svec!["hostname"]), false)
-        .unwrap(),
-      run: Permissions::new_unary(&None, &Some(svec!["deno"]), false).unwrap(),
       all: Permissions::new_all(false),
     };
     let perms4 = Permissions {
       read: Permissions::new_unary(
-        &Some(vec![]),
-        &Some(vec![PathBuf::from("/foo")]),
+        Some(&[]),
+        Some(&[PathBuf::from("/foo")]),
         false,
       )
       .unwrap(),
       write: Permissions::new_unary(
-        &Some(vec![]),
-        &Some(vec![PathBuf::from("/foo")]),
+        Some(&[]),
+        Some(&[PathBuf::from("/foo")]),
         false,
       )
       .unwrap(),
       ffi: Permissions::new_unary(
-        &Some(vec![]),
-        &Some(vec![PathBuf::from("/foo")]),
+        Some(&[]),
+        Some(&[PathBuf::from("/foo")]),
         false,
       )
       .unwrap(),
       net: Permissions::new_unary(
-        &Some(vec![]),
-        &Some(svec!["127.0.0.1:8000"]),
+        Some(&[]),
+        Some(&sarr!["127.0.0.1:8000"]),
         false,
       )
       .unwrap(),
-      env: Permissions::new_unary(&Some(vec![]), &Some(svec!["HOME"]), false)
+      env: Permissions::new_unary(Some(&[]), Some(&sarr!["HOME"]), false)
         .unwrap(),
-      sys: Permissions::new_unary(
-        &Some(vec![]),
-        &Some(svec!["hostname"]),
+      sys: Permissions::new_unary(Some(&[]), Some(&sarr!["hostname"]), false)
+        .unwrap(),
+      run: Permissions::new_unary(
+        Some(&[]),
+        Some(&["deno".to_string().into()]),
         false,
       )
       .unwrap(),
-      run: Permissions::new_unary(&Some(vec![]), &Some(svec!["deno"]), false)
-        .unwrap(),
       all: Permissions::new_all(false),
     };
     #[rustfmt::skip]
@@ -2894,33 +2916,38 @@ mod tests {
     set_prompter(Box::new(TestPrompter));
     let mut perms = Permissions {
       read: Permissions::new_unary(
-        &Some(vec![PathBuf::from("/foo"), PathBuf::from("/foo/baz")]),
-        &None,
+        Some(&[PathBuf::from("/foo"), PathBuf::from("/foo/baz")]),
+        None,
         false,
       )
       .unwrap(),
       write: Permissions::new_unary(
-        &Some(vec![PathBuf::from("/foo"), PathBuf::from("/foo/baz")]),
-        &None,
+        Some(&[PathBuf::from("/foo"), PathBuf::from("/foo/baz")]),
+        None,
         false,
       )
       .unwrap(),
       ffi: Permissions::new_unary(
-        &Some(vec![PathBuf::from("/foo"), PathBuf::from("/foo/baz")]),
-        &None,
+        Some(&[PathBuf::from("/foo"), PathBuf::from("/foo/baz")]),
+        None,
         false,
       )
       .unwrap(),
       net: Permissions::new_unary(
-        &Some(svec!["127.0.0.1", "127.0.0.1:8000"]),
-        &None,
+        Some(&sarr!["127.0.0.1", "127.0.0.1:8000"]),
+        None,
         false,
       )
       .unwrap(),
-      env: Permissions::new_unary(&Some(svec!["HOME"]), &None, false).unwrap(),
-      sys: Permissions::new_unary(&Some(svec!["hostname"]), &None, false)
+      env: Permissions::new_unary(Some(&sarr!["HOME"]), None, false).unwrap(),
+      sys: Permissions::new_unary(Some(&sarr!["hostname"]), None, false)
         .unwrap(),
-      run: Permissions::new_unary(&Some(svec!["deno"]), &None, false).unwrap(),
+      run: Permissions::new_unary(
+        Some(&["deno".to_string().into()]),
+        None,
+        false,
+      )
+      .unwrap(),
       all: Permissions::new_all(false),
     };
     #[rustfmt::skip]
@@ -3006,11 +3033,13 @@ mod tests {
       .check(&NetDescriptor("deno.land".parse().unwrap(), None), None)
       .is_err());
 
+    #[allow(clippy::disallowed_methods)]
+    let cwd = std::env::current_dir().unwrap();
     prompt_value.set(true);
-    assert!(perms.run.check("cat", None).is_ok());
+    assert!(perms.run.check(&cwd.join("cat"), None).is_ok());
     prompt_value.set(false);
-    assert!(perms.run.check("cat", None).is_ok());
-    assert!(perms.run.check("ls", None).is_err());
+    assert!(perms.run.check(&cwd.join("cat"), None).is_ok());
+    assert!(perms.run.check(&cwd.join("ls"), None).is_err());
 
     prompt_value.set(true);
     assert!(perms.env.check("HOME", None).is_ok());
@@ -3102,12 +3131,14 @@ mod tests {
       .is_ok());
 
     prompt_value.set(false);
-    assert!(perms.run.check("cat", None).is_err());
+    #[allow(clippy::disallowed_methods)]
+    let cwd = std::env::current_dir().unwrap();
+    assert!(perms.run.check(&cwd.join("cat"), None).is_err());
     prompt_value.set(true);
-    assert!(perms.run.check("cat", None).is_err());
-    assert!(perms.run.check("ls", None).is_ok());
+    assert!(perms.run.check(&cwd.join("cat"), None).is_err());
+    assert!(perms.run.check(&cwd.join("ls"), None).is_ok());
     prompt_value.set(false);
-    assert!(perms.run.check("ls", None).is_ok());
+    assert!(perms.run.check(&cwd.join("ls"), None).is_ok());
 
     prompt_value.set(false);
     assert!(perms.env.check("HOME", None).is_err());
@@ -3134,7 +3165,7 @@ mod tests {
     let mut perms = Permissions::allow_all();
     perms.env = UnaryPermission {
       granted_global: false,
-      ..Permissions::new_unary(&Some(svec!["HOME"]), &None, false).unwrap()
+      ..Permissions::new_unary(Some(&sarr!["HOME"]), None, false).unwrap()
     };
 
     prompt_value.set(true);
@@ -3150,14 +3181,14 @@ mod tests {
   fn test_check_partial_denied() {
     let mut perms = Permissions {
       read: Permissions::new_unary(
-        &Some(vec![]),
-        &Some(vec![PathBuf::from("/foo/bar")]),
+        Some(&[]),
+        Some(&[PathBuf::from("/foo/bar")]),
         false,
       )
       .unwrap(),
       write: Permissions::new_unary(
-        &Some(vec![]),
-        &Some(vec![PathBuf::from("/foo/bar")]),
+        Some(&[]),
+        Some(&[PathBuf::from("/foo/bar")]),
         false,
       )
       .unwrap(),
@@ -3175,8 +3206,8 @@ mod tests {
   fn test_net_fully_qualified_domain_name() {
     let mut perms = Permissions {
       net: Permissions::new_unary(
-        &Some(vec!["allowed.domain".to_string(), "1.1.1.1".to_string()]),
-        &Some(vec!["denied.domain".to_string(), "2.2.2.2".to_string()]),
+        Some(&["allowed.domain".to_string(), "1.1.1.1".to_string()]),
+        Some(&["denied.domain".to_string(), "2.2.2.2".to_string()]),
         false,
       )
       .unwrap(),
@@ -3341,8 +3372,8 @@ mod tests {
   fn test_create_child_permissions() {
     set_prompter(Box::new(TestPrompter));
     let mut main_perms = Permissions {
-      env: Permissions::new_unary(&Some(vec![]), &None, false).unwrap(),
-      net: Permissions::new_unary(&Some(svec!["foo", "bar"]), &None, false)
+      env: Permissions::new_unary(Some(&[]), None, false).unwrap(),
+      net: Permissions::new_unary(Some(&sarr!["foo", "bar"]), None, false)
         .unwrap(),
       ..Permissions::none_without_prompt()
     };
@@ -3358,8 +3389,8 @@ mod tests {
       )
       .unwrap(),
       Permissions {
-        env: Permissions::new_unary(&Some(vec![]), &None, false).unwrap(),
-        net: Permissions::new_unary(&Some(svec!["foo"]), &None, false).unwrap(),
+        env: Permissions::new_unary(Some(&[]), None, false).unwrap(),
+        net: Permissions::new_unary(Some(&sarr!["foo"]), None, false).unwrap(),
         ..Permissions::none_without_prompt()
       }
     );
@@ -3445,20 +3476,20 @@ mod tests {
     set_prompter(Box::new(TestPrompter));
 
     assert!(Permissions::new_unary::<ReadDescriptor>(
-      &Some(vec![Default::default()]),
-      &None,
+      Some(&[Default::default()]),
+      None,
       false
     )
     .is_err());
     assert!(Permissions::new_unary::<EnvDescriptor>(
-      &Some(vec![Default::default()]),
-      &None,
+      Some(&[Default::default()]),
+      None,
       false
     )
     .is_err());
     assert!(Permissions::new_unary::<NetDescriptor>(
-      &Some(vec![Default::default()]),
-      &None,
+      Some(&[Default::default()]),
+      None,
       false
     )
     .is_err());
diff --git a/tests/integration/run_tests.rs b/tests/integration/run_tests.rs
index 841ef2d182d9be..47fcdb657bd541 100644
--- a/tests/integration/run_tests.rs
+++ b/tests/integration/run_tests.rs
@@ -3683,11 +3683,6 @@ itest!(followup_dyn_import_resolved {
   output: "run/followup_dyn_import_resolves/main.ts.out",
 });
 
-itest!(allow_run_allowlist_resolution {
-  args: "run --quiet -A allow_run_allowlist_resolution.ts",
-  output: "allow_run_allowlist_resolution.ts.out",
-});
-
 itest!(unhandled_rejection {
   args: "run --check run/unhandled_rejection.ts",
   output: "run/unhandled_rejection.ts.out",
@@ -4592,16 +4587,32 @@ fn permission_prompt_escapes_ansi_codes_and_control_chars() {
     ))
   });
 
-  util::with_pty(&["repl"], |mut console| {
-    console.write_line_raw(r#"const boldANSI = "\u001b[1m";"#);
-    console.expect("undefined");
-    console.write_line_raw(r#"const unboldANSI = "\u001b[22m";"#);
-    console.expect("undefined");
-    console.write_line_raw(
-      r#"new Deno.Command(`${boldANSI}cat${unboldANSI}`).spawn();"#,
-    );
-    console.expect("\u{250f} \u{26a0}\u{fe0f}  Deno requests run access to \"\\u{1b}[1mcat\\u{1b}[22m\".");
-  });
+  // windows doesn't support backslashes in paths, so just try this on unix
+  if cfg!(unix) {
+    let context = TestContextBuilder::default().use_temp_cwd().build();
+    context
+      .new_command()
+      .env("PATH", context.temp_dir().path())
+      .env("DYLD_FALLBACK_LIBRARY_PATH", "")
+      .env("LD_LIBRARY_PATH", "")
+      .args_vec(["repl", "--allow-write=."])
+      .with_pty(|mut console| {
+        console.write_line_raw(r#"const boldANSI = "\u001b[1m";"#);
+        console.expect("undefined");
+        console.write_line_raw(r#"const unboldANSI = "\u001b[22m";"#);
+        console.expect("undefined");
+        console.write_line_raw(
+          r#"Deno.writeTextFileSync(`${boldANSI}cat${unboldANSI}`, "");"#,
+        );
+        console.expect("undefined");
+        console.write_line_raw(
+          r#"new Deno.Command(`./${boldANSI}cat${unboldANSI}`).spawn();"#,
+        );
+        console
+          .expect("\u{250f} \u{26a0}\u{fe0f}  Deno requests run access to \"");
+        console.expect("\\u{1b}[1mcat\\u{1b}[22m\"."); // ensure escaped
+      });
+  }
 }
 
 itest!(node_builtin_modules_ts {
diff --git a/tests/specs/compile/permissions_denied/__test__.jsonc b/tests/specs/compile/permissions_denied/__test__.jsonc
index 8f85901628a553..ec683ea62e3f59 100644
--- a/tests/specs/compile/permissions_denied/__test__.jsonc
+++ b/tests/specs/compile/permissions_denied/__test__.jsonc
@@ -1,5 +1,9 @@
 {
   "tempDir": true,
+  "envs": {
+    "DYLD_FALLBACK_LIBRARY_PATH": "",
+    "LD_LIBRARY_PATH": ""
+  },
   "steps": [{
     "if": "unix",
     "args": "compile --output main main.ts",
diff --git a/tests/specs/compile/permissions_denied/main.out b/tests/specs/compile/permissions_denied/main.out
index e9ea45c812aede..47a4707cc7cdbf 100644
--- a/tests/specs/compile/permissions_denied/main.out
+++ b/tests/specs/compile/permissions_denied/main.out
@@ -1,2 +1,2 @@
-error: Uncaught (in promise) PermissionDenied: Requires run access to "deno", specify the required permissions during compilation using `deno compile --allow-run`
+error: Uncaught (in promise) PermissionDenied: Requires run access to "[WILDLINE]deno[WILDLINE]", specify the required permissions during compilation using `deno compile --allow-run`
 [WILDCARD]
\ No newline at end of file
diff --git a/tests/specs/npm/lifecycle_scripts/node_gyp_not_found.out b/tests/specs/npm/lifecycle_scripts/node_gyp_not_found.out
index 65ea53d586f60a..2f0ff11e287035 100644
--- a/tests/specs/npm/lifecycle_scripts/node_gyp_not_found.out
+++ b/tests/specs/npm/lifecycle_scripts/node_gyp_not_found.out
@@ -3,6 +3,6 @@ Download http://localhost:4260/@denotest/node-addon-implicit-node-gyp
 Download http://localhost:4260/@denotest/node-addon-implicit-node-gyp/1.0.0.tgz
 Initialize @denotest/node-addon-implicit-node-gyp@1.0.0
 [UNORDERED_END]
-warning: node-gyp was used in a script, but was not listed as a dependency. Either add it as a dependency or install it globally (e.g. `npm install -g node-gyp`)
+Warning node-gyp was used in a script, but was not listed as a dependency. Either add it as a dependency or install it globally (e.g. `npm install -g node-gyp`)
 [WILDCARD]
 error: script 'install' in '@denotest/node-addon-implicit-node-gyp@1.0.0' failed with exit code 1
diff --git a/tests/specs/permission/path_not_permitted/__test__.jsonc b/tests/specs/permission/path_not_permitted/__test__.jsonc
new file mode 100644
index 00000000000000..f10e8b389ea558
--- /dev/null
+++ b/tests/specs/permission/path_not_permitted/__test__.jsonc
@@ -0,0 +1,10 @@
+{
+  "tempDir": true,
+  "envs": {
+    "LD_LIBRARY_PATH": "",
+    "LD_PRELOAD": "",
+    "DYLD_FALLBACK_LIBRARY_PATH": ""
+  },
+  "args": "run -A main.ts",
+  "output": "main.out"
+}
diff --git a/tests/specs/permission/path_not_permitted/main.out b/tests/specs/permission/path_not_permitted/main.out
new file mode 100644
index 00000000000000..3817c2ca51c58e
--- /dev/null
+++ b/tests/specs/permission/path_not_permitted/main.out
@@ -0,0 +1,11 @@
+Running...
+PermissionDenied: Requires run access to "[WILDLINE]deno[WILDLINE]", run again with the --allow-run flag
+    [WILDCARD]
+    at file:///[WILDLINE]/sub.ts:15:5 {
+  name: "PermissionDenied"
+}
+PermissionDenied: Requires run access to "[WILDLINE]deno[WILDLINE]", run again with the --allow-run flag
+    [WILDCARD]
+    at file:///[WILDLINE]/sub.ts:23:22 {
+  name: "PermissionDenied"
+}
diff --git a/tests/specs/permission/path_not_permitted/main.ts b/tests/specs/permission/path_not_permitted/main.ts
new file mode 100644
index 00000000000000..9e8d627f2ae445
--- /dev/null
+++ b/tests/specs/permission/path_not_permitted/main.ts
@@ -0,0 +1,18 @@
+const binaryName = Deno.build.os === "windows" ? "deno.exe" : "deno";
+Deno.copyFileSync(Deno.execPath(), binaryName);
+
+console.log("Running...");
+new Deno.Command(
+  Deno.execPath(),
+  {
+    args: [
+      "run",
+      "--allow-write",
+      "--allow-read",
+      `--allow-run=${binaryName}`,
+      "sub.ts",
+    ],
+    stderr: "inherit",
+    stdout: "inherit",
+  },
+).outputSync();
diff --git a/tests/specs/permission/path_not_permitted/sub.ts b/tests/specs/permission/path_not_permitted/sub.ts
new file mode 100644
index 00000000000000..f2b6d6b37c769d
--- /dev/null
+++ b/tests/specs/permission/path_not_permitted/sub.ts
@@ -0,0 +1,34 @@
+const binaryName = Deno.build.os === "windows" ? "deno.exe" : "deno";
+const pathSep = Deno.build.os === "windows" ? "\\" : "/";
+
+Deno.mkdirSync("subdir");
+Deno.copyFileSync(binaryName, "subdir/" + binaryName);
+
+try {
+  const commandResult = new Deno.Command(
+    binaryName,
+    {
+      env: { "PATH": Deno.cwd() + pathSep + "subdir" },
+      stdout: "inherit",
+      stderr: "inherit",
+    },
+  ).outputSync();
+
+  console.log(commandResult.code);
+} catch (err) {
+  console.log(err);
+}
+
+try {
+  const child = Deno.run(
+    {
+      cmd: [binaryName],
+      env: { "PATH": Deno.cwd() + pathSep + "subdir" },
+      stdout: "inherit",
+      stderr: "inherit",
+    },
+  );
+  console.log((await child.status()).code);
+} catch (err) {
+  console.log(err);
+}
diff --git a/tests/specs/permission/write_allow_binary/__test__.jsonc b/tests/specs/permission/write_allow_binary/__test__.jsonc
new file mode 100644
index 00000000000000..a47fed572dcd24
--- /dev/null
+++ b/tests/specs/permission/write_allow_binary/__test__.jsonc
@@ -0,0 +1,5 @@
+{
+  "tempDir": true,
+  "args": "run -A main.ts",
+  "output": "main.out"
+}
diff --git a/tests/specs/permission/write_allow_binary/main.out b/tests/specs/permission/write_allow_binary/main.out
new file mode 100644
index 00000000000000..e7c47f2883de40
--- /dev/null
+++ b/tests/specs/permission/write_allow_binary/main.out
@@ -0,0 +1,6 @@
+Running...
+error: Uncaught (in promise) PermissionDenied: Requires write access to "binary[WILDLINE]", run again with the --allow-write flag
+Deno.writeTextFileSync(binaryName, "");
+     ^
+    at [WILDCARD]
+    at file:///[WILDLINE]sub.ts:3:6
diff --git a/tests/specs/permission/write_allow_binary/main.ts b/tests/specs/permission/write_allow_binary/main.ts
new file mode 100644
index 00000000000000..73deeab9a7bbf0
--- /dev/null
+++ b/tests/specs/permission/write_allow_binary/main.ts
@@ -0,0 +1,14 @@
+const binaryName = Deno.build.os === "windows" ? "binary.exe" : "binary";
+Deno.copyFileSync(Deno.execPath(), binaryName);
+
+console.log("Running...");
+const result = new Deno.Command(
+  Deno.execPath(),
+  {
+    args: ["run", "--allow-write", `--allow-run=./${binaryName}`, "sub.ts"],
+    stderr: "inherit",
+    stdout: "inherit",
+  },
+).outputSync();
+
+console.assert(result.code == 1, "Expected failure");
diff --git a/tests/specs/permission/write_allow_binary/sub.ts b/tests/specs/permission/write_allow_binary/sub.ts
new file mode 100644
index 00000000000000..e865597b15749d
--- /dev/null
+++ b/tests/specs/permission/write_allow_binary/sub.ts
@@ -0,0 +1,3 @@
+const binaryName = Deno.build.os === "windows" ? "binary.exe" : "binary";
+
+Deno.writeTextFileSync(binaryName, "");
diff --git a/tests/specs/run/allow_run_allowlist_resolution/__test__.jsonc b/tests/specs/run/allow_run_allowlist_resolution/__test__.jsonc
new file mode 100644
index 00000000000000..173e13027fc347
--- /dev/null
+++ b/tests/specs/run/allow_run_allowlist_resolution/__test__.jsonc
@@ -0,0 +1,8 @@
+{
+  "args": "run --quiet -A main.ts",
+  "output": "main.out",
+  "envs": {
+    "DYLD_FALLBACK_LIBRARY_PATH": "",
+    "LD_LIBRARY_PATH": ""
+  }
+}
diff --git a/tests/testdata/allow_run_allowlist_resolution.ts.out b/tests/specs/run/allow_run_allowlist_resolution/main.out
similarity index 67%
rename from tests/testdata/allow_run_allowlist_resolution.ts.out
rename to tests/specs/run/allow_run_allowlist_resolution/main.out
index 16ba6754a92111..f61f9b55030ec2 100644
--- a/tests/testdata/allow_run_allowlist_resolution.ts.out
+++ b/tests/specs/run/allow_run_allowlist_resolution/main.out
@@ -1,15 +1,15 @@
 PermissionStatus { state: "granted", onchange: null }
-PermissionStatus { state: "granted", onchange: null }
-PermissionStatus { state: "granted", onchange: null }
-PermissionStatus { state: "granted", onchange: null }
-
 PermissionStatus { state: "granted", onchange: null }
 PermissionStatus { state: "prompt", onchange: null }
 PermissionStatus { state: "granted", onchange: null }
+---
+Info Failed to resolve 'deno' for allow-run: cannot find binary path
+PermissionStatus { state: "prompt", onchange: null }
+PermissionStatus { state: "prompt", onchange: null }
+PermissionStatus { state: "prompt", onchange: null }
 PermissionStatus { state: "prompt", onchange: null }
-
+---
 PermissionStatus { state: "granted", onchange: null }
 PermissionStatus { state: "granted", onchange: null }
 PermissionStatus { state: "prompt", onchange: null }
 PermissionStatus { state: "granted", onchange: null }
-
diff --git a/tests/testdata/allow_run_allowlist_resolution.ts b/tests/specs/run/allow_run_allowlist_resolution/main.ts
similarity index 71%
rename from tests/testdata/allow_run_allowlist_resolution.ts
rename to tests/specs/run/allow_run_allowlist_resolution/main.ts
index c7369d928a097a..bf33d8cbe10a05 100644
--- a/tests/testdata/allow_run_allowlist_resolution.ts
+++ b/tests/specs/run/allow_run_allowlist_resolution/main.ts
@@ -1,26 +1,26 @@
 // Testing the following (but with `deno` instead of `echo`):
 // | `deno run --allow-run=echo`         | `which path == "/usr/bin/echo"` at startup | `which path != "/usr/bin/echo"` at startup |
 // |-------------------------------------|--------------------------------------------|--------------------------------------------|
-// | **`Deno.Command("echo")`**          | ✅                                          | ✅                                          |
-// | **`Deno.Command("/usr/bin/echo")`** | ✅                                          | ❌                                          |
+// | **`Deno.Command("echo")`**          | ✅                                          | ✅                                         |
+// | **`Deno.Command("/usr/bin/echo")`** | ✅                                          | ❌                                         |
 
 // | `deno run --allow-run=/usr/bin/echo | `which path == "/usr/bin/echo"` at runtime | `which path != "/usr/bin/echo"` at runtime |
 // |-------------------------------------|--------------------------------------------|--------------------------------------------|
-// | **`Deno.Command("echo")`**          | ✅                                          | ❌                                          |
-// | **`Deno.Command("/usr/bin/echo")`** | ✅                                          | ✅                                          |
+// | **`Deno.Command("echo")`**          | ✅                                          | ❌                                         |
+// | **`Deno.Command("/usr/bin/echo")`** | ✅                                          | ✅                                         |
 
 const execPath = Deno.execPath();
 const execPathParent = execPath.replace(/[/\\][^/\\]+$/, "");
 
 const testUrl = `data:application/typescript;base64,${
   btoa(`
-  console.log(await Deno.permissions.query({ name: "run", command: "deno" }));
-  console.log(await Deno.permissions.query({ name: "run", command: "${
+  console.error(await Deno.permissions.query({ name: "run", command: "deno" }));
+  console.error(await Deno.permissions.query({ name: "run", command: "${
     execPath.replaceAll("\\", "\\\\")
   }" }));
   Deno.env.set("PATH", "");
-  console.log(await Deno.permissions.query({ name: "run", command: "deno" }));
-  console.log(await Deno.permissions.query({ name: "run", command: "${
+  console.error(await Deno.permissions.query({ name: "run", command: "deno" }));
+  console.error(await Deno.permissions.query({ name: "run", command: "${
     execPath.replaceAll("\\", "\\\\")
   }" }));
 `)
@@ -29,38 +29,39 @@ const testUrl = `data:application/typescript;base64,${
 const process1 = await new Deno.Command(Deno.execPath(), {
   args: [
     "run",
-    "--quiet",
     "--allow-env",
     "--allow-run=deno",
     testUrl,
   ],
-  stderr: "null",
+  stdout: "inherit",
+  stderr: "inherit",
   env: { "PATH": execPathParent },
 }).output();
-console.log(new TextDecoder().decode(process1.stdout));
 
-const process2 = await new Deno.Command(Deno.execPath(), {
+console.error("---");
+
+await new Deno.Command(Deno.execPath(), {
   args: [
     "run",
-    "--quiet",
     "--allow-env",
     "--allow-run=deno",
     testUrl,
   ],
-  stderr: "null",
+  stderr: "inherit",
+  stdout: "inherit",
   env: { "PATH": "" },
 }).output();
-console.log(new TextDecoder().decode(process2.stdout));
 
-const process3 = await new Deno.Command(Deno.execPath(), {
+console.error("---");
+
+await new Deno.Command(Deno.execPath(), {
   args: [
     "run",
-    "--quiet",
     "--allow-env",
     `--allow-run=${execPath}`,
     testUrl,
   ],
-  stderr: "null",
+  stderr: "inherit",
+  stdout: "inherit",
   env: { "PATH": execPathParent },
 }).output();
-console.log(new TextDecoder().decode(process3.stdout));
diff --git a/tests/specs/run/ld_preload/__test__.jsonc b/tests/specs/run/ld_preload/__test__.jsonc
index 767e423d063055..882f157e9e0f9c 100644
--- a/tests/specs/run/ld_preload/__test__.jsonc
+++ b/tests/specs/run/ld_preload/__test__.jsonc
@@ -7,13 +7,11 @@
   "tests": {
     "env_arg": {
       "args": "run --allow-run=echo env_arg.ts",
-      "output": "env_arg.out",
-      "exitCode": 1
+      "output": "env_arg.out"
     },
     "set_with_allow_env": {
       "args": "run --allow-run=echo --allow-env set_with_allow_env.ts",
-      "output": "set_with_allow_env.out",
-      "exitCode": 1
+      "output": "set_with_allow_env.out"
     }
   }
 }
diff --git a/tests/specs/run/ld_preload/env_arg.out b/tests/specs/run/ld_preload/env_arg.out
index fbf37014ae78b4..3df781a8e6a7d5 100644
--- a/tests/specs/run/ld_preload/env_arg.out
+++ b/tests/specs/run/ld_preload/env_arg.out
@@ -1,4 +1,8 @@
-error: Uncaught (in promise) PermissionDenied: Requires --allow-all permissions to spawn subprocess with LD_PRELOAD environment variable.
-}).spawn();
-   ^
-    at [WILDCARD]
+PermissionDenied: Requires --allow-all permissions to spawn subprocess with LD_PRELOAD environment variable.
+    [WILDCARD]
+  name: "PermissionDenied"
+}
+PermissionDenied: Requires --allow-all permissions to spawn subprocess with LD_PRELOAD environment variable.
+    [WILDCARD]
+  name: "PermissionDenied"
+}
diff --git a/tests/specs/run/ld_preload/env_arg.ts b/tests/specs/run/ld_preload/env_arg.ts
index 0b236619e109dc..d7ca1073dfa088 100644
--- a/tests/specs/run/ld_preload/env_arg.ts
+++ b/tests/specs/run/ld_preload/env_arg.ts
@@ -1,5 +1,20 @@
-const output = new Deno.Command("echo", {
-  env: {
-    "LD_PRELOAD": "./libpreload.so",
-  },
-}).spawn();
+try {
+  new Deno.Command("echo", {
+    env: {
+      "LD_PRELOAD": "./libpreload.so",
+    },
+  }).spawn();
+} catch (err) {
+  console.log(err);
+}
+
+try {
+  Deno.run({
+    cmd: ["echo"],
+    env: {
+      "LD_PRELOAD": "./libpreload.so",
+    },
+  });
+} catch (err) {
+  console.log(err);
+}
diff --git a/tests/specs/run/ld_preload/set_with_allow_env.out b/tests/specs/run/ld_preload/set_with_allow_env.out
index 2e92763ddac227..60dba7cff1e78d 100644
--- a/tests/specs/run/ld_preload/set_with_allow_env.out
+++ b/tests/specs/run/ld_preload/set_with_allow_env.out
@@ -1,4 +1,8 @@
-error: Uncaught (in promise) PermissionDenied: Requires --allow-all permissions to spawn subprocess with LD_PRELOAD environment variable.
-const output = new Deno.Command("echo").spawn();
-                                        ^
-    at [WILDCARD]
+PermissionDenied: Requires --allow-all permissions to spawn subprocess with LD_PRELOAD environment variable.
+  [WILDCARD]
+  name: "PermissionDenied"
+}
+PermissionDenied: Requires --allow-all permissions to spawn subprocess with DYLD_FALLBACK_LIBRARY_PATH, LD_PRELOAD environment variables.
+  [WILDCARD]
+  name: "PermissionDenied"
+}
diff --git a/tests/specs/run/ld_preload/set_with_allow_env.ts b/tests/specs/run/ld_preload/set_with_allow_env.ts
index 9530f4478c5ede..79004aa1656ecf 100644
--- a/tests/specs/run/ld_preload/set_with_allow_env.ts
+++ b/tests/specs/run/ld_preload/set_with_allow_env.ts
@@ -1,3 +1,15 @@
 Deno.env.set("LD_PRELOAD", "./libpreload.so");
 
-const output = new Deno.Command("echo").spawn();
+try {
+  new Deno.Command("echo").spawn();
+} catch (err) {
+  console.log(err);
+}
+
+Deno.env.set("DYLD_FALLBACK_LIBRARY_PATH", "./libpreload.so");
+
+try {
+  Deno.run({ cmd: ["echo"] }).spawnSync();
+} catch (err) {
+  console.log(err);
+}
diff --git a/tests/testdata/run/089_run_allow_list.ts.out b/tests/testdata/run/089_run_allow_list.ts.out
index 68a4a2ac578a61..0fc1c80c2a948d 100644
--- a/tests/testdata/run/089_run_allow_list.ts.out
+++ b/tests/testdata/run/089_run_allow_list.ts.out
@@ -1,3 +1,3 @@
-[WILDCARD]PermissionDenied: Requires run access to "ls", run again with the --allow-run flag
+[WILDCARD]PermissionDenied: Requires run access to "[WILDLINE]ls[WILDLINE]", run again with the --allow-run flag
 [WILDCARD]
 true
diff --git a/tests/unit/process_test.ts b/tests/unit/process_test.ts
index a35362d090feb8..383f17f384252b 100644
--- a/tests/unit/process_test.ts
+++ b/tests/unit/process_test.ts
@@ -611,6 +611,6 @@ Deno.test(
     p.close();
     p.stdout.close();
     assertStrictEquals(code, 1);
-    assertStringIncludes(stderr, "Failed getting cwd.");
+    assertStringIncludes(stderr, "failed resolving cwd:");
   },
 );
diff --git a/tools/lint.js b/tools/lint.js
index d40b1b1fd92827..08b551e984dd33 100755
--- a/tools/lint.js
+++ b/tools/lint.js
@@ -221,7 +221,7 @@ async function ensureNoNewITests() {
     "pm_tests.rs": 0,
     "publish_tests.rs": 0,
     "repl_tests.rs": 0,
-    "run_tests.rs": 351,
+    "run_tests.rs": 350,
     "shared_library_tests.rs": 0,
     "task_tests.rs": 30,
     "test_tests.rs": 75,