diff --git a/crates/worker-runtime/src/worker_backend.rs b/crates/worker-runtime/src/worker_backend.rs
index 4949a899..1fcf9c06 100644
--- a/crates/worker-runtime/src/worker_backend.rs
+++ b/crates/worker-runtime/src/worker_backend.rs
@@ -1703,11 +1703,7 @@ mod tests {
         runtime_base: &std::path::Path,
         working_directory_id: &str,
     ) -> PathBuf {
-        runtime_base
-            .join("working-directories")
-            .join(working_directory_id)
-            .join("root")
-            .join("repo-main")
+        runtime_base.join(working_directory_id).join("checkout")
     }
 
     #[test]
@@ -2008,7 +2004,7 @@ mod tests {
         let error = runtime.create_worker(request).unwrap_err();
 
         assert!(format!("{error:?}").contains("spawn failed"));
-        let working_directories_root = runtime_base.path().join("working-directories");
+        let working_directories_root = runtime_base.path();
         let remaining_entries = fs::read_dir(working_directories_root)
             .map(|entries| entries.count())
             .unwrap_or(0);
diff --git a/crates/worker-runtime/src/working_directory.rs b/crates/worker-runtime/src/working_directory.rs
index ebbec7fc..10bcd593 100644
--- a/crates/worker-runtime/src/working_directory.rs
+++ b/crates/worker-runtime/src/working_directory.rs
@@ -10,7 +10,7 @@ use std::process::Command;
 use std::sync::atomic::{AtomicU64, Ordering};
 use std::time::{SystemTime, UNIX_EPOCH};
 
-const WORKING_DIRECTORIES_DIR: &str = "working-directories";
+const CHECKOUT_DIR: &str = "checkout";
 const MATERIALIZATION_RECORD: &str = "materialization.json";
 static NEXT_WORKING_DIRECTORY_SEQUENCE: AtomicU64 = AtomicU64::new(0);
 
@@ -200,9 +200,7 @@ impl LocalGitWorktreeMaterializer {
     }
 
     fn working_directory_root(&self, working_directory_id: &str) -> PathBuf {
-        self.runtime_root
-            .join(WORKING_DIRECTORIES_DIR)
-            .join(working_directory_id)
+        self.runtime_root.join(working_directory_id)
     }
 
     fn corrupted_status(&self, working_directory_id: &str) -> WorkingDirectoryStatus {
@@ -346,9 +344,7 @@ impl LocalGitWorktreeMaterializer {
             .filter(|value| !value.is_empty());
 
         let working_directory_root = self.working_directory_root(&working_directory_id);
-        let worktree_root = working_directory_root
-            .join("root")
-            .join(sanitize_path_component(&request.repository.id));
+        let worktree_root = working_directory_root.join(CHECKOUT_DIR);
         if worktree_root.exists() {
             return Err(WorkingDirectoryDiagnostic::new(
                 "working_directory_exists",
@@ -455,8 +451,7 @@ impl WorkingDirectoryMaterializer for LocalGitWorktreeMaterializer {
     fn list_working_directories(
         &self,
     ) -> Result<Vec<WorkingDirectoryStatus>, WorkingDirectoryDiagnostic> {
-        let root = self.runtime_root.join(WORKING_DIRECTORIES_DIR);
-        let entries = match fs::read_dir(&root) {
+        let entries = match fs::read_dir(&self.runtime_root) {
             Ok(entries) => entries,
             Err(error) if error.kind() == std::io::ErrorKind::NotFound => return Ok(Vec::new()),
             Err(_) => {
@@ -800,6 +795,17 @@ mod tests {
             .unwrap();
 
         assert!(binding.root.starts_with(runtime_root.path()));
+        assert_eq!(
+            binding.working_directory_root(),
+            runtime_root
+                .path()
+                .join(&binding.working_directory.id)
+                .as_path()
+        );
+        assert_eq!(
+            binding.root(),
+            binding.working_directory_root().join(CHECKOUT_DIR)
+        );
         assert!(binding.root.join("README.md").exists());
         let branch = git_stdout(binding.root(), ["branch", "--show-current"]).unwrap();
         assert!(
diff --git a/web/workspace/src/lib/workspace/console/model.test.ts b/web/workspace/src/lib/workspace/console/model.test.ts
index 9b031f29..d1c5253c 100644
--- a/web/workspace/src/lib/workspace/console/model.test.ts
+++ b/web/workspace/src/lib/workspace/console/model.test.ts
@@ -323,7 +323,7 @@ Deno.test("projectConsole shows Grep query and caps result preview to five entri
 
 Deno.test("projectConsole keeps Grep error detail in the body", () => {
   const message =
-    "Tool execution failed: Invalid argument: path is outside allowed scope: /home/hare/.yoi/workdirs/working-directories/0019f5bce74f1000000/root/main/ghq.local/github/openai/codex";
+    "Tool execution failed: Invalid argument: path is outside allowed scope: /home/hare/.yoi/workdirs/0019f5bce74f1000000/checkout/ghq.local/github/openai/codex";
   const projection = projectConsole([
     {
       eventId: "74",