diff --git a/internal/cli/run.go b/internal/cli/run.go
index d5aff9178..da3679af7 100644
--- a/internal/cli/run.go
+++ b/internal/cli/run.go
@@ -1266,7 +1266,13 @@ func runAgent(ctx context.Context, agentName, fullsendDir, outputBase, targetRep
 
 		// 9d. Extract target repo back to host. SafeDownload removes dangerous
 		// symlinks (absolute or repo-escaping) and .git/hooks/ to prevent sandbox escape.
-		if clearErr := os.RemoveAll(hostRepositoryDir); clearErr != nil {
+		//
+		// Clear the contents of the directory rather than removing the directory
+		// itself. Removing the directory would invalidate the inode, which breaks
+		// any shell whose CWD points at it (the next command in that shell would
+		// fail with "getwd: no such file or directory").
+		printer.StepInfo(fmt.Sprintf("Clearing %s before extraction", hostRepositoryDir))
+		if clearErr := clearDirContents(hostRepositoryDir); clearErr != nil {
 			return fmt.Errorf("clearing local repo %s before extraction: %w", hostRepositoryDir, clearErr)
 		}
 		repoExtractStart := time.Now()
@@ -2972,3 +2978,19 @@ func containedLocalPath(baseDir, source string) (string, error) {
 	}
 	return real, nil
 }
+
+// clearDirContents removes all entries inside dir without removing dir itself.
+// This preserves the directory inode so that shells whose CWD points at dir
+// continue to work after the call.
+func clearDirContents(dir string) error {
+	entries, err := os.ReadDir(dir)
+	if err != nil {
+		return err
+	}
+	for _, e := range entries {
+		if err := os.RemoveAll(filepath.Join(dir, e.Name())); err != nil {
+			return err
+		}
+	}
+	return nil
+}
diff --git a/internal/cli/run_test.go b/internal/cli/run_test.go
index f43fa1630..00b24cb1e 100644
--- a/internal/cli/run_test.go
+++ b/internal/cli/run_test.go
@@ -3494,6 +3494,47 @@ func TestRunAgent_StatusNotifierSetup(t *testing.T) {
 	assert.Contains(t, err.Error(), "openshell")
 }
 
+func TestClearDirContents(t *testing.T) {
+	t.Run("populated directory", func(t *testing.T) {
+		dir := t.TempDir()
+
+		// Create some files and a subdirectory.
+		require.NoError(t, os.WriteFile(filepath.Join(dir, "a.txt"), []byte("a"), 0o644))
+		require.NoError(t, os.Mkdir(filepath.Join(dir, "sub"), 0o755))
+		require.NoError(t, os.WriteFile(filepath.Join(dir, "sub", "b.txt"), []byte("b"), 0o644))
+
+		// Grab inode before clearing.
+		infoBefore, err := os.Stat(dir)
+		require.NoError(t, err)
+
+		require.NoError(t, clearDirContents(dir))
+
+		// Directory itself still exists with the same inode.
+		infoAfter, err := os.Stat(dir)
+		require.NoError(t, err)
+		assert.True(t, os.SameFile(infoBefore, infoAfter), "directory inode should be preserved")
+
+		// Contents are gone.
+		entries, err := os.ReadDir(dir)
+		require.NoError(t, err)
+		assert.Empty(t, entries)
+	})
+
+	t.Run("empty directory", func(t *testing.T) {
+		dir := t.TempDir()
+		require.NoError(t, clearDirContents(dir))
+
+		entries, err := os.ReadDir(dir)
+		require.NoError(t, err)
+		assert.Empty(t, entries)
+	})
+
+	t.Run("non-existent directory", func(t *testing.T) {
+		err := clearDirContents(filepath.Join(t.TempDir(), "does-not-exist"))
+		require.Error(t, err)
+	})
+}
+
 func TestResolveBackendFromConfigData_OrgConfig(t *testing.T) {
 	t.Parallel()