fix(core) RequestPermissions + ApplyPatch (#14055)

## Summary
The apply_patch tool should also respect AdditionalPermissions

## Testing
- [x] Added unit tests

---------

Co-authored-by: Codex <noreply@openai.com>

codex-rs/core/src/tools/handlers/apply_patch.rs

@@ -18,6 +18,7 @@ use crate::tools::context::ToolOutput;
 use crate::tools::context::ToolPayload;
 use crate::tools::events::ToolEmitter;
 use crate::tools::events::ToolEventCtx;
+use crate::tools::handlers::apply_granted_turn_permissions;
 use crate::tools::handlers::parse_arguments;
 use crate::tools::orchestrator::ToolOrchestrator;
 use crate::tools::registry::ToolHandler;
@@ -30,7 +31,10 @@ use crate::tools::spec::JsonSchema;
 use async_trait::async_trait;
 use codex_apply_patch::ApplyPatchAction;
 use codex_apply_patch::ApplyPatchFileChange;
+use codex_protocol::models::FileSystemPermissions;
+use codex_protocol::models::PermissionProfile;
 use codex_utils_absolute_path::AbsolutePathBuf;
+use std::collections::BTreeSet;
 use std::sync::Arc;
 
 pub struct ApplyPatchHandler;
@@ -61,6 +65,31 @@ fn to_abs_path(cwd: &Path, path: &Path) -> Option<AbsolutePathBuf> {
     AbsolutePathBuf::resolve_path_against_base(path, cwd).ok()
 }
 
+fn write_permissions_for_paths(file_paths: &[AbsolutePathBuf]) -> Option<PermissionProfile> {
+    let write_paths = file_paths
+        .iter()
+        .map(|path| {
+            path.parent()
+                .unwrap_or_else(|| path.clone())
+                .into_path_buf()
+        })
+        .collect::<BTreeSet<_>>()
+        .into_iter()
+        .map(AbsolutePathBuf::from_absolute_path)
+        .collect::<Result<Vec<_>, _>>()
+        .ok()?;
+
+    let permissions = (!write_paths.is_empty()).then_some(PermissionProfile {
+        file_system: Some(FileSystemPermissions {
+            read: Some(vec![]),
+            write: Some(write_paths),
+        }),
+        ..Default::default()
+    })?;
+
+    crate::sandboxing::normalize_additional_permissions(permissions).ok()
+}
+
 #[async_trait]
 impl ToolHandler for ApplyPatchHandler {
     fn kind(&self) -> ToolKind {
@@ -119,6 +148,12 @@ impl ToolHandler for ApplyPatchHandler {
                     InternalApplyPatchInvocation::DelegateToExec(apply) => {
                         let changes = convert_apply_patch_to_protocol(&apply.action);
                         let file_paths = file_paths_for_action(&apply.action);
+                        let effective_additional_permissions = apply_granted_turn_permissions(
+                            session.as_ref(),
+                            crate::sandboxing::SandboxPermissions::UseDefault,
+                            write_permissions_for_paths(&file_paths),
+                        )
+                        .await;
                         let emitter =
                             ToolEmitter::apply_patch(changes.clone(), apply.auto_approved);
                         let event_ctx = ToolEventCtx::new(
@@ -134,6 +169,12 @@ impl ToolHandler for ApplyPatchHandler {
                             file_paths,
                             changes,
                             exec_approval_requirement: apply.exec_approval_requirement,
+                            sandbox_permissions: effective_additional_permissions
+                                .sandbox_permissions,
+                            additional_permissions: effective_additional_permissions
+                                .additional_permissions,
+                            permissions_preapproved: effective_additional_permissions
+                                .permissions_preapproved,
                             timeout_ms: None,
                             codex_exe: turn.codex_linux_sandbox_exe.clone(),
                         };
@@ -222,6 +263,12 @@ pub(crate) async fn intercept_apply_patch(
                 InternalApplyPatchInvocation::DelegateToExec(apply) => {
                     let changes = convert_apply_patch_to_protocol(&apply.action);
                     let approval_keys = file_paths_for_action(&apply.action);
+                    let effective_additional_permissions = apply_granted_turn_permissions(
+                        session.as_ref(),
+                        crate::sandboxing::SandboxPermissions::UseDefault,
+                        write_permissions_for_paths(&approval_keys),
+                    )
+                    .await;
                     let emitter = ToolEmitter::apply_patch(changes.clone(), apply.auto_approved);
                     let event_ctx = ToolEventCtx::new(
                         session.as_ref(),
@@ -236,6 +283,11 @@ pub(crate) async fn intercept_apply_patch(
                         file_paths: approval_keys,
                         changes,
                         exec_approval_requirement: apply.exec_approval_requirement,
+                        sandbox_permissions: effective_additional_permissions.sandbox_permissions,
+                        additional_permissions: effective_additional_permissions
+                            .additional_permissions,
+                        permissions_preapproved: effective_additional_permissions
+                            .permissions_preapproved,
                         timeout_ms,
                         codex_exe: turn.codex_linux_sandbox_exe.clone(),
                     };

codex-rs/core/src/tools/runtimes/apply_patch.rs

@@ -23,6 +23,7 @@ use crate::tools::sandboxing::ToolRuntime;
 use crate::tools::sandboxing::with_cached_approval;
 use codex_apply_patch::ApplyPatchAction;
 use codex_apply_patch::CODEX_CORE_APPLY_PATCH_ARG1;
+use codex_protocol::models::PermissionProfile;
 use codex_protocol::protocol::AskForApproval;
 use codex_protocol::protocol::FileChange;
 use codex_protocol::protocol::ReviewDecision;
@@ -37,6 +38,9 @@ pub struct ApplyPatchRequest {
     pub file_paths: Vec<AbsolutePathBuf>,
     pub changes: std::collections::HashMap<PathBuf, FileChange>,
     pub exec_approval_requirement: ExecApprovalRequirement,
+    pub sandbox_permissions: SandboxPermissions,
+    pub additional_permissions: Option<PermissionProfile>,
+    pub permissions_preapproved: bool,
     pub timeout_ms: Option<u64>,
     pub codex_exe: Option<PathBuf>,
 }
@@ -87,8 +91,8 @@ impl ApplyPatchRuntime {
             expiration: req.timeout_ms.into(),
             // Run apply_patch with a minimal environment for determinism and to avoid leaks.
             env: HashMap::new(),
-            sandbox_permissions: SandboxPermissions::UseDefault,
-            additional_permissions: None,
+            sandbox_permissions: req.sandbox_permissions,
+            additional_permissions: req.additional_permissions.clone(),
             justification: None,
         })
     }
@@ -134,6 +138,9 @@ impl Approvable<ApplyPatchRequest> for ApplyPatchRuntime {
                 let action = ApplyPatchRuntime::build_guardian_review_request(req);
                 return review_approval_request(session, turn, action, retry_reason).await;
             }
+            if req.permissions_preapproved && retry_reason.is_none() {
+                return ReviewDecision::Approved;
+            }
             if let Some(reason) = retry_reason {
                 let rx_approve = session
                     .request_patch_approval(turn, call_id, changes.clone(), Some(reason), None)
@@ -244,6 +251,9 @@ mod tests {
                 reason: None,
                 proposed_execpolicy_amendment: None,
             },
+            sandbox_permissions: SandboxPermissions::UseDefault,
+            additional_permissions: None,
+            permissions_preapproved: false,
             timeout_ms: None,
             codex_exe: None,
         };