chore: split apply_patch logic out of codex.rs and into apply_patch.rs (#1703)

This is a straight refactor, moving apply-patch-related code from
`codex.rs` and into the new `apply_patch.rs` file. The only "logical"
change is inlining `#[allow(clippy::unwrap_used)]` instead of declaring
`#![allow(clippy::unwrap_used)]` at the top of the file (which is
currently the case in `codex.rs`).

---
[//]: # (BEGIN SAPLING FOOTER)
Stack created with [Sapling](https://sapling-scm.com). Best reviewed
with [ReviewStack](https://reviewstack.dev/openai/codex/pull/1703).
* #1705
* __->__ #1703
* #1702
* #1698
* #1697

codex-rs/core/src/apply_patch.rs

@@ -0,0 +1,406 @@
+use crate::codex::Session;
+use crate::models::FunctionCallOutputPayload;
+use crate::models::ResponseInputItem;
+use crate::protocol::Event;
+use crate::protocol::EventMsg;
+use crate::protocol::FileChange;
+use crate::protocol::PatchApplyBeginEvent;
+use crate::protocol::PatchApplyEndEvent;
+use crate::protocol::ReviewDecision;
+use crate::safety::SafetyCheck;
+use crate::safety::assess_patch_safety;
+use anyhow::Context;
+use codex_apply_patch::AffectedPaths;
+use codex_apply_patch::ApplyPatchAction;
+use codex_apply_patch::ApplyPatchFileChange;
+use codex_apply_patch::print_summary;
+use std::collections::HashMap;
+use std::path::Path;
+use std::path::PathBuf;
+
+pub(crate) async fn apply_patch(
+    sess: &Session,
+    sub_id: String,
+    call_id: String,
+    action: ApplyPatchAction,
+) -> ResponseInputItem {
+    let writable_roots_snapshot = {
+        #[allow(clippy::unwrap_used)]
+        let guard = sess.writable_roots.lock().unwrap();
+        guard.clone()
+    };
+
+    let auto_approved = match assess_patch_safety(
+        &action,
+        sess.approval_policy,
+        &writable_roots_snapshot,
+        &sess.cwd,
+    ) {
+        SafetyCheck::AutoApprove { .. } => true,
+        SafetyCheck::AskUser => {
+            // Compute a readable summary of path changes to include in the
+            // approval request so the user can make an informed decision.
+            let rx_approve = sess
+                .request_patch_approval(sub_id.clone(), call_id.clone(), &action, None, None)
+                .await;
+            match rx_approve.await.unwrap_or_default() {
+                ReviewDecision::Approved | ReviewDecision::ApprovedForSession => false,
+                ReviewDecision::Denied | ReviewDecision::Abort => {
+                    return ResponseInputItem::FunctionCallOutput {
+                        call_id,
+                        output: FunctionCallOutputPayload {
+                            content: "patch rejected by user".to_string(),
+                            success: Some(false),
+                        },
+                    };
+                }
+            }
+        }
+        SafetyCheck::Reject { reason } => {
+            return ResponseInputItem::FunctionCallOutput {
+                call_id,
+                output: FunctionCallOutputPayload {
+                    content: format!("patch rejected: {reason}"),
+                    success: Some(false),
+                },
+            };
+        }
+    };
+
+    // Verify write permissions before touching the filesystem.
+    let writable_snapshot = {
+        #[allow(clippy::unwrap_used)]
+        sess.writable_roots.lock().unwrap().clone()
+    };
+
+    if let Some(offending) = first_offending_path(&action, &writable_snapshot, &sess.cwd) {
+        let root = offending.parent().unwrap_or(&offending).to_path_buf();
+
+        let reason = Some(format!(
+            "grant write access to {} for this session",
+            root.display()
+        ));
+
+        let rx = sess
+            .request_patch_approval(
+                sub_id.clone(),
+                call_id.clone(),
+                &action,
+                reason.clone(),
+                Some(root.clone()),
+            )
+            .await;
+
+        if !matches!(
+            rx.await.unwrap_or_default(),
+            ReviewDecision::Approved | ReviewDecision::ApprovedForSession
+        ) {
+            return ResponseInputItem::FunctionCallOutput {
+                call_id,
+                output: FunctionCallOutputPayload {
+                    content: "patch rejected by user".to_string(),
+                    success: Some(false),
+                },
+            };
+        }
+
+        // user approved, extend writable roots for this session
+        #[allow(clippy::unwrap_used)]
+        sess.writable_roots.lock().unwrap().push(root);
+    }
+
+    let _ = sess
+        .tx_event
+        .send(Event {
+            id: sub_id.clone(),
+            msg: EventMsg::PatchApplyBegin(PatchApplyBeginEvent {
+                call_id: call_id.clone(),
+                auto_approved,
+                changes: convert_apply_patch_to_protocol(&action),
+            }),
+        })
+        .await;
+
+    let mut stdout = Vec::new();
+    let mut stderr = Vec::new();
+    // Enforce writable roots. If a write is blocked, collect offending root
+    // and prompt the user to extend permissions.
+    let mut result = apply_changes_from_apply_patch_and_report(&action, &mut stdout, &mut stderr);
+
+    if let Err(err) = &result {
+        if err.kind() == std::io::ErrorKind::PermissionDenied {
+            // Determine first offending path.
+            let offending_opt = action
+                .changes()
+                .iter()
+                .flat_map(|(path, change)| match change {
+                    ApplyPatchFileChange::Add { .. } => vec![path.as_ref()],
+                    ApplyPatchFileChange::Delete => vec![path.as_ref()],
+                    ApplyPatchFileChange::Update {
+                        move_path: Some(move_path),
+                        ..
+                    } => {
+                        vec![path.as_ref(), move_path.as_ref()]
+                    }
+                    ApplyPatchFileChange::Update {
+                        move_path: None, ..
+                    } => vec![path.as_ref()],
+                })
+                .find_map(|path: &Path| {
+                    // ApplyPatchAction promises to guarantee absolute paths.
+                    if !path.is_absolute() {
+                        panic!("apply_patch invariant failed: path is not absolute: {path:?}");
+                    }
+
+                    let writable = {
+                        #[allow(clippy::unwrap_used)]
+                        let roots = sess.writable_roots.lock().unwrap();
+                        roots.iter().any(|root| path.starts_with(root))
+                    };
+                    if writable {
+                        None
+                    } else {
+                        Some(path.to_path_buf())
+                    }
+                });
+
+            if let Some(offending) = offending_opt {
+                let root = offending.parent().unwrap_or(&offending).to_path_buf();
+
+                let reason = Some(format!(
+                    "grant write access to {} for this session",
+                    root.display()
+                ));
+                let rx = sess
+                    .request_patch_approval(
+                        sub_id.clone(),
+                        call_id.clone(),
+                        &action,
+                        reason.clone(),
+                        Some(root.clone()),
+                    )
+                    .await;
+                if matches!(
+                    rx.await.unwrap_or_default(),
+                    ReviewDecision::Approved | ReviewDecision::ApprovedForSession
+                ) {
+                    // Extend writable roots.
+                    #[allow(clippy::unwrap_used)]
+                    sess.writable_roots.lock().unwrap().push(root);
+                    stdout.clear();
+                    stderr.clear();
+                    result = apply_changes_from_apply_patch_and_report(
+                        &action,
+                        &mut stdout,
+                        &mut stderr,
+                    );
+                }
+            }
+        }
+    }
+
+    // Emit PatchApplyEnd event.
+    let success_flag = result.is_ok();
+    let _ = sess
+        .tx_event
+        .send(Event {
+            id: sub_id.clone(),
+            msg: EventMsg::PatchApplyEnd(PatchApplyEndEvent {
+                call_id: call_id.clone(),
+                stdout: String::from_utf8_lossy(&stdout).to_string(),
+                stderr: String::from_utf8_lossy(&stderr).to_string(),
+                success: success_flag,
+            }),
+        })
+        .await;
+
+    match result {
+        Ok(_) => ResponseInputItem::FunctionCallOutput {
+            call_id,
+            output: FunctionCallOutputPayload {
+                content: String::from_utf8_lossy(&stdout).to_string(),
+                success: None,
+            },
+        },
+        Err(e) => ResponseInputItem::FunctionCallOutput {
+            call_id,
+            output: FunctionCallOutputPayload {
+                content: format!("error: {e:#}, stderr: {}", String::from_utf8_lossy(&stderr)),
+                success: Some(false),
+            },
+        },
+    }
+}
+
+/// Return the first path in `hunks` that is NOT under any of the
+/// `writable_roots` (after normalising). If all paths are acceptable,
+/// returns None.
+fn first_offending_path(
+    action: &ApplyPatchAction,
+    writable_roots: &[PathBuf],
+    cwd: &Path,
+) -> Option<PathBuf> {
+    let changes = action.changes();
+    for (path, change) in changes {
+        let candidate = match change {
+            ApplyPatchFileChange::Add { .. } => path,
+            ApplyPatchFileChange::Delete => path,
+            ApplyPatchFileChange::Update { move_path, .. } => move_path.as_ref().unwrap_or(path),
+        };
+
+        let abs = if candidate.is_absolute() {
+            candidate.clone()
+        } else {
+            cwd.join(candidate)
+        };
+
+        let mut allowed = false;
+        for root in writable_roots {
+            let root_abs = if root.is_absolute() {
+                root.clone()
+            } else {
+                cwd.join(root)
+            };
+            if abs.starts_with(&root_abs) {
+                allowed = true;
+                break;
+            }
+        }
+
+        if !allowed {
+            return Some(candidate.clone());
+        }
+    }
+    None
+}
+
+pub(crate) fn convert_apply_patch_to_protocol(
+    action: &ApplyPatchAction,
+) -> HashMap<PathBuf, FileChange> {
+    let changes = action.changes();
+    let mut result = HashMap::with_capacity(changes.len());
+    for (path, change) in changes {
+        let protocol_change = match change {
+            ApplyPatchFileChange::Add { content } => FileChange::Add {
+                content: content.clone(),
+            },
+            ApplyPatchFileChange::Delete => FileChange::Delete,
+            ApplyPatchFileChange::Update {
+                unified_diff,
+                move_path,
+                new_content: _new_content,
+            } => FileChange::Update {
+                unified_diff: unified_diff.clone(),
+                move_path: move_path.clone(),
+            },
+        };
+        result.insert(path.clone(), protocol_change);
+    }
+    result
+}
+
+fn apply_changes_from_apply_patch_and_report(
+    action: &ApplyPatchAction,
+    stdout: &mut impl std::io::Write,
+    stderr: &mut impl std::io::Write,
+) -> std::io::Result<()> {
+    match apply_changes_from_apply_patch(action) {
+        Ok(affected_paths) => {
+            print_summary(&affected_paths, stdout)?;
+        }
+        Err(err) => {
+            writeln!(stderr, "{err:?}")?;
+        }
+    }
+
+    Ok(())
+}
+
+fn apply_changes_from_apply_patch(action: &ApplyPatchAction) -> anyhow::Result<AffectedPaths> {
+    let mut added: Vec<PathBuf> = Vec::new();
+    let mut modified: Vec<PathBuf> = Vec::new();
+    let mut deleted: Vec<PathBuf> = Vec::new();
+
+    let changes = action.changes();
+    for (path, change) in changes {
+        match change {
+            ApplyPatchFileChange::Add { content } => {
+                if let Some(parent) = path.parent() {
+                    if !parent.as_os_str().is_empty() {
+                        std::fs::create_dir_all(parent).with_context(|| {
+                            format!("Failed to create parent directories for {}", path.display())
+                        })?;
+                    }
+                }
+                std::fs::write(path, content)
+                    .with_context(|| format!("Failed to write file {}", path.display()))?;
+                added.push(path.clone());
+            }
+            ApplyPatchFileChange::Delete => {
+                std::fs::remove_file(path)
+                    .with_context(|| format!("Failed to delete file {}", path.display()))?;
+                deleted.push(path.clone());
+            }
+            ApplyPatchFileChange::Update {
+                unified_diff: _unified_diff,
+                move_path,
+                new_content,
+            } => {
+                if let Some(move_path) = move_path {
+                    if let Some(parent) = move_path.parent() {
+                        if !parent.as_os_str().is_empty() {
+                            std::fs::create_dir_all(parent).with_context(|| {
+                                format!(
+                                    "Failed to create parent directories for {}",
+                                    move_path.display()
+                                )
+                            })?;
+                        }
+                    }
+
+                    std::fs::rename(path, move_path)
+                        .with_context(|| format!("Failed to rename file {}", path.display()))?;
+                    std::fs::write(move_path, new_content)?;
+                    modified.push(move_path.clone());
+                    deleted.push(path.clone());
+                } else {
+                    std::fs::write(path, new_content)?;
+                    modified.push(path.clone());
+                }
+            }
+        }
+    }
+
+    Ok(AffectedPaths {
+        added,
+        modified,
+        deleted,
+    })
+}
+
+pub(crate) fn get_writable_roots(cwd: &Path) -> Vec<PathBuf> {
+    let mut writable_roots = Vec::new();
+    if cfg!(target_os = "macos") {
+        // On macOS, $TMPDIR is private to the user.
+        writable_roots.push(std::env::temp_dir());
+
+        // Allow pyenv to update its shims directory. Without this, any tool
+        // that happens to be managed by `pyenv` will fail with an error like:
+        //
+        //   pyenv: cannot rehash: $HOME/.pyenv/shims isn't writable
+        //
+        // which is emitted every time `pyenv` tries to run `rehash` (for
+        // example, after installing a new Python package that drops an entry
+        // point). Although the sandbox is intentionally read‑only by default,
+        // writing to the user's local `pyenv` directory is safe because it
+        // is already user‑writable and scoped to the current user account.
+        if let Ok(home_dir) = std::env::var("HOME") {
+            let pyenv_dir = PathBuf::from(home_dir).join(".pyenv");
+            writable_roots.push(pyenv_dir);
+        }
+    }
+
+    writable_roots.push(cwd.to_path_buf());
+
+    writable_roots
+}

codex-rs/core/src/codex.rs

@@ -4,22 +4,17 @@
 use std::borrow::Cow;
 use std::collections::HashMap;
 use std::collections::HashSet;
-use std::path::Path;
 use std::path::PathBuf;
 use std::sync::Arc;
 use std::sync::Mutex;
 use std::sync::atomic::AtomicU64;
 use std::time::Duration;
 
-use anyhow::Context;
 use async_channel::Receiver;
 use async_channel::Sender;
-use codex_apply_patch::AffectedPaths;
 use codex_apply_patch::ApplyPatchAction;
-use codex_apply_patch::ApplyPatchFileChange;
 use codex_apply_patch::MaybeApplyPatchVerified;
 use codex_apply_patch::maybe_parse_apply_patch_verified;
-use codex_apply_patch::print_summary;
 use futures::prelude::*;
 use mcp_types::CallToolResult;
 use serde::Serialize;
@@ -34,6 +29,9 @@ use tracing::trace;
 use tracing::warn;
 use uuid::Uuid;
 
+use crate::apply_patch::convert_apply_patch_to_protocol;
+use crate::apply_patch::get_writable_roots;
+use crate::apply_patch::{self};
 use crate::client::ModelClient;
 use crate::client_common::Prompt;
 use crate::client_common::ResponseEvent;
@@ -71,11 +69,8 @@ use crate::protocol::EventMsg;
 use crate::protocol::ExecApprovalRequestEvent;
 use crate::protocol::ExecCommandBeginEvent;
 use crate::protocol::ExecCommandEndEvent;
-use crate::protocol::FileChange;
 use crate::protocol::InputItem;
 use crate::protocol::Op;
-use crate::protocol::PatchApplyBeginEvent;
-use crate::protocol::PatchApplyEndEvent;
 use crate::protocol::ReviewDecision;
 use crate::protocol::SandboxPolicy;
 use crate::protocol::SessionConfiguredEvent;
@@ -84,7 +79,6 @@ use crate::protocol::TaskCompleteEvent;
 use crate::rollout::RolloutRecorder;
 use crate::safety::SafetyCheck;
 use crate::safety::assess_command_safety;
-use crate::safety::assess_patch_safety;
 use crate::shell;
 use crate::user_notification::UserNotification;
 use crate::util::backoff;
@@ -189,19 +183,19 @@ impl Codex {
 /// A session has at most 1 running task at a time, and can be interrupted by user input.
 pub(crate) struct Session {
     client: ModelClient,
-    tx_event: Sender<Event>,
+    pub(crate) tx_event: Sender<Event>,
     ctrl_c: Arc<Notify>,
 
     /// The session's current working directory. All relative paths provided by
     /// the model as well as sandbox policies are resolved against this path
     /// instead of `std::env::current_dir()`.
-    cwd: PathBuf,
+    pub(crate) cwd: PathBuf,
     base_instructions: Option<String>,
     user_instructions: Option<String>,
-    approval_policy: AskForApproval,
+    pub(crate) approval_policy: AskForApproval,
     sandbox_policy: SandboxPolicy,
     shell_environment_policy: ShellEnvironmentPolicy,
-    writable_roots: Mutex<Vec<PathBuf>>,
+    pub(crate) writable_roots: Mutex<Vec<PathBuf>>,
     disable_response_storage: bool,
 
     /// Manager for external MCP servers/tools.
@@ -1419,7 +1413,7 @@ async fn handle_container_exec_with_params(
     // check if this was a patch, and apply it if so
     match maybe_parse_apply_patch_verified(&params.command, &params.cwd) {
         MaybeApplyPatchVerified::Body(changes) => {
-            return apply_patch(sess, sub_id, call_id, changes).await;
+            return apply_patch::apply_patch(sess, sub_id, call_id, changes).await;
         }
         MaybeApplyPatchVerified::CorrectnessError(parse_error) => {
             // It looks like an invocation of `apply_patch`, but we
@@ -1668,384 +1662,6 @@ async fn handle_sandbox_error(
     }
 }
 
-async fn apply_patch(
-    sess: &Session,
-    sub_id: String,
-    call_id: String,
-    action: ApplyPatchAction,
-) -> ResponseInputItem {
-    let writable_roots_snapshot = {
-        let guard = sess.writable_roots.lock().unwrap();
-        guard.clone()
-    };
-
-    let auto_approved = match assess_patch_safety(
-        &action,
-        sess.approval_policy,
-        &writable_roots_snapshot,
-        &sess.cwd,
-    ) {
-        SafetyCheck::AutoApprove { .. } => true,
-        SafetyCheck::AskUser => {
-            // Compute a readable summary of path changes to include in the
-            // approval request so the user can make an informed decision.
-            let rx_approve = sess
-                .request_patch_approval(sub_id.clone(), call_id.clone(), &action, None, None)
-                .await;
-            match rx_approve.await.unwrap_or_default() {
-                ReviewDecision::Approved | ReviewDecision::ApprovedForSession => false,
-                ReviewDecision::Denied | ReviewDecision::Abort => {
-                    return ResponseInputItem::FunctionCallOutput {
-                        call_id,
-                        output: FunctionCallOutputPayload {
-                            content: "patch rejected by user".to_string(),
-                            success: Some(false),
-                        },
-                    };
-                }
-            }
-        }
-        SafetyCheck::Reject { reason } => {
-            return ResponseInputItem::FunctionCallOutput {
-                call_id,
-                output: FunctionCallOutputPayload {
-                    content: format!("patch rejected: {reason}"),
-                    success: Some(false),
-                },
-            };
-        }
-    };
-
-    // Verify write permissions before touching the filesystem.
-    let writable_snapshot = { sess.writable_roots.lock().unwrap().clone() };
-
-    if let Some(offending) = first_offending_path(&action, &writable_snapshot, &sess.cwd) {
-        let root = offending.parent().unwrap_or(&offending).to_path_buf();
-
-        let reason = Some(format!(
-            "grant write access to {} for this session",
-            root.display()
-        ));
-
-        let rx = sess
-            .request_patch_approval(
-                sub_id.clone(),
-                call_id.clone(),
-                &action,
-                reason.clone(),
-                Some(root.clone()),
-            )
-            .await;
-
-        if !matches!(
-            rx.await.unwrap_or_default(),
-            ReviewDecision::Approved | ReviewDecision::ApprovedForSession
-        ) {
-            return ResponseInputItem::FunctionCallOutput {
-                call_id,
-                output: FunctionCallOutputPayload {
-                    content: "patch rejected by user".to_string(),
-                    success: Some(false),
-                },
-            };
-        }
-
-        // user approved, extend writable roots for this session
-        sess.writable_roots.lock().unwrap().push(root);
-    }
-
-    let _ = sess
-        .tx_event
-        .send(Event {
-            id: sub_id.clone(),
-            msg: EventMsg::PatchApplyBegin(PatchApplyBeginEvent {
-                call_id: call_id.clone(),
-                auto_approved,
-                changes: convert_apply_patch_to_protocol(&action),
-            }),
-        })
-        .await;
-
-    let mut stdout = Vec::new();
-    let mut stderr = Vec::new();
-    // Enforce writable roots. If a write is blocked, collect offending root
-    // and prompt the user to extend permissions.
-    let mut result = apply_changes_from_apply_patch_and_report(&action, &mut stdout, &mut stderr);
-
-    if let Err(err) = &result {
-        if err.kind() == std::io::ErrorKind::PermissionDenied {
-            // Determine first offending path.
-            let offending_opt = action
-                .changes()
-                .iter()
-                .flat_map(|(path, change)| match change {
-                    ApplyPatchFileChange::Add { .. } => vec![path.as_ref()],
-                    ApplyPatchFileChange::Delete => vec![path.as_ref()],
-                    ApplyPatchFileChange::Update {
-                        move_path: Some(move_path),
-                        ..
-                    } => {
-                        vec![path.as_ref(), move_path.as_ref()]
-                    }
-                    ApplyPatchFileChange::Update {
-                        move_path: None, ..
-                    } => vec![path.as_ref()],
-                })
-                .find_map(|path: &Path| {
-                    // ApplyPatchAction promises to guarantee absolute paths.
-                    if !path.is_absolute() {
-                        panic!("apply_patch invariant failed: path is not absolute: {path:?}");
-                    }
-
-                    let writable = {
-                        let roots = sess.writable_roots.lock().unwrap();
-                        roots.iter().any(|root| path.starts_with(root))
-                    };
-                    if writable {
-                        None
-                    } else {
-                        Some(path.to_path_buf())
-                    }
-                });
-
-            if let Some(offending) = offending_opt {
-                let root = offending.parent().unwrap_or(&offending).to_path_buf();
-
-                let reason = Some(format!(
-                    "grant write access to {} for this session",
-                    root.display()
-                ));
-                let rx = sess
-                    .request_patch_approval(
-                        sub_id.clone(),
-                        call_id.clone(),
-                        &action,
-                        reason.clone(),
-                        Some(root.clone()),
-                    )
-                    .await;
-                if matches!(
-                    rx.await.unwrap_or_default(),
-                    ReviewDecision::Approved | ReviewDecision::ApprovedForSession
-                ) {
-                    // Extend writable roots.
-                    sess.writable_roots.lock().unwrap().push(root);
-                    stdout.clear();
-                    stderr.clear();
-                    result = apply_changes_from_apply_patch_and_report(
-                        &action,
-                        &mut stdout,
-                        &mut stderr,
-                    );
-                }
-            }
-        }
-    }
-
-    // Emit PatchApplyEnd event.
-    let success_flag = result.is_ok();
-    let _ = sess
-        .tx_event
-        .send(Event {
-            id: sub_id.clone(),
-            msg: EventMsg::PatchApplyEnd(PatchApplyEndEvent {
-                call_id: call_id.clone(),
-                stdout: String::from_utf8_lossy(&stdout).to_string(),
-                stderr: String::from_utf8_lossy(&stderr).to_string(),
-                success: success_flag,
-            }),
-        })
-        .await;
-
-    match result {
-        Ok(_) => ResponseInputItem::FunctionCallOutput {
-            call_id,
-            output: FunctionCallOutputPayload {
-                content: String::from_utf8_lossy(&stdout).to_string(),
-                success: None,
-            },
-        },
-        Err(e) => ResponseInputItem::FunctionCallOutput {
-            call_id,
-            output: FunctionCallOutputPayload {
-                content: format!("error: {e:#}, stderr: {}", String::from_utf8_lossy(&stderr)),
-                success: Some(false),
-            },
-        },
-    }
-}
-
-/// Return the first path in `hunks` that is NOT under any of the
-/// `writable_roots` (after normalising). If all paths are acceptable,
-/// returns None.
-fn first_offending_path(
-    action: &ApplyPatchAction,
-    writable_roots: &[PathBuf],
-    cwd: &Path,
-) -> Option<PathBuf> {
-    let changes = action.changes();
-    for (path, change) in changes {
-        let candidate = match change {
-            ApplyPatchFileChange::Add { .. } => path,
-            ApplyPatchFileChange::Delete => path,
-            ApplyPatchFileChange::Update { move_path, .. } => move_path.as_ref().unwrap_or(path),
-        };
-
-        let abs = if candidate.is_absolute() {
-            candidate.clone()
-        } else {
-            cwd.join(candidate)
-        };
-
-        let mut allowed = false;
-        for root in writable_roots {
-            let root_abs = if root.is_absolute() {
-                root.clone()
-            } else {
-                cwd.join(root)
-            };
-            if abs.starts_with(&root_abs) {
-                allowed = true;
-                break;
-            }
-        }
-
-        if !allowed {
-            return Some(candidate.clone());
-        }
-    }
-    None
-}
-
-fn convert_apply_patch_to_protocol(action: &ApplyPatchAction) -> HashMap<PathBuf, FileChange> {
-    let changes = action.changes();
-    let mut result = HashMap::with_capacity(changes.len());
-    for (path, change) in changes {
-        let protocol_change = match change {
-            ApplyPatchFileChange::Add { content } => FileChange::Add {
-                content: content.clone(),
-            },
-            ApplyPatchFileChange::Delete => FileChange::Delete,
-            ApplyPatchFileChange::Update {
-                unified_diff,
-                move_path,
-                new_content: _new_content,
-            } => FileChange::Update {
-                unified_diff: unified_diff.clone(),
-                move_path: move_path.clone(),
-            },
-        };
-        result.insert(path.clone(), protocol_change);
-    }
-    result
-}
-
-fn apply_changes_from_apply_patch_and_report(
-    action: &ApplyPatchAction,
-    stdout: &mut impl std::io::Write,
-    stderr: &mut impl std::io::Write,
-) -> std::io::Result<()> {
-    match apply_changes_from_apply_patch(action) {
-        Ok(affected_paths) => {
-            print_summary(&affected_paths, stdout)?;
-        }
-        Err(err) => {
-            writeln!(stderr, "{err:?}")?;
-        }
-    }
-
-    Ok(())
-}
-
-fn apply_changes_from_apply_patch(action: &ApplyPatchAction) -> anyhow::Result<AffectedPaths> {
-    let mut added: Vec<PathBuf> = Vec::new();
-    let mut modified: Vec<PathBuf> = Vec::new();
-    let mut deleted: Vec<PathBuf> = Vec::new();
-
-    let changes = action.changes();
-    for (path, change) in changes {
-        match change {
-            ApplyPatchFileChange::Add { content } => {
-                if let Some(parent) = path.parent() {
-                    if !parent.as_os_str().is_empty() {
-                        std::fs::create_dir_all(parent).with_context(|| {
-                            format!("Failed to create parent directories for {}", path.display())
-                        })?;
-                    }
-                }
-                std::fs::write(path, content)
-                    .with_context(|| format!("Failed to write file {}", path.display()))?;
-                added.push(path.clone());
-            }
-            ApplyPatchFileChange::Delete => {
-                std::fs::remove_file(path)
-                    .with_context(|| format!("Failed to delete file {}", path.display()))?;
-                deleted.push(path.clone());
-            }
-            ApplyPatchFileChange::Update {
-                unified_diff: _unified_diff,
-                move_path,
-                new_content,
-            } => {
-                if let Some(move_path) = move_path {
-                    if let Some(parent) = move_path.parent() {
-                        if !parent.as_os_str().is_empty() {
-                            std::fs::create_dir_all(parent).with_context(|| {
-                                format!(
-                                    "Failed to create parent directories for {}",
-                                    move_path.display()
-                                )
-                            })?;
-                        }
-                    }
-
-                    std::fs::rename(path, move_path)
-                        .with_context(|| format!("Failed to rename file {}", path.display()))?;
-                    std::fs::write(move_path, new_content)?;
-                    modified.push(move_path.clone());
-                    deleted.push(path.clone());
-                } else {
-                    std::fs::write(path, new_content)?;
-                    modified.push(path.clone());
-                }
-            }
-        }
-    }
-
-    Ok(AffectedPaths {
-        added,
-        modified,
-        deleted,
-    })
-}
-
-fn get_writable_roots(cwd: &Path) -> Vec<PathBuf> {
-    let mut writable_roots = Vec::new();
-    if cfg!(target_os = "macos") {
-        // On macOS, $TMPDIR is private to the user.
-        writable_roots.push(std::env::temp_dir());
-
-        // Allow pyenv to update its shims directory. Without this, any tool
-        // that happens to be managed by `pyenv` will fail with an error like:
-        //
-        //   pyenv: cannot rehash: $HOME/.pyenv/shims isn't writable
-        //
-        // which is emitted every time `pyenv` tries to run `rehash` (for
-        // example, after installing a new Python package that drops an entry
-        // point). Although the sandbox is intentionally read‑only by default,
-        // writing to the user's local `pyenv` directory is safe because it
-        // is already user‑writable and scoped to the current user account.
-        if let Ok(home_dir) = std::env::var("HOME") {
-            let pyenv_dir = PathBuf::from(home_dir).join(".pyenv");
-            writable_roots.push(pyenv_dir);
-        }
-    }
-
-    writable_roots.push(cwd.to_path_buf());
-
-    writable_roots
-}
-
 /// Exec output is a pre-serialized JSON payload
 fn format_exec_output(output: &str, exit_code: i32, duration: Duration) -> String {
     #[derive(Serialize)]

codex-rs/core/src/lib.rs

@@ -5,6 +5,7 @@
 // the TUI or the tracing stack).
 #![deny(clippy::print_stdout, clippy::print_stderr)]
 
+mod apply_patch;
 mod bash;
 mod chat_completions;
 mod client;