fix(persistence): FlushAndAck is a durability barrier that reports lost writes

The persistence actor acked FlushAndAck unconditionally after writing its
pending merged notification: nothing was fsynced and every storage failure
was only warn-logged, so persist_ack, the reconnect flush and history
repair treated lost writes as persisted.

The barrier now writes the pending notification, reports the first storage
failure latched since the last barrier (every actor arm latches), and
fsyncs the whole session directory tree (files, directories, deletions).
Session directories are created durably (init and fork copy), and the
shared summary writer syncs its staged bytes before publishing and the
parent afterwards, so a concurrent /rename cannot publish unsynced bytes
over a synced summary.json. FlushComplete and the persist_ack, history
repair and end-of-turn callers propagate the io::Result; CopyFile fails on
a sync error but keeps the latch for the barrier.

Ported from upstream 1.0.1x (grok-build persistence.rs pending_write_error
+ durable storage helpers), reshaped without the dirty-file set.

Claude-Session: https://claude.ai/code/session_01RUqV8HVGXcAETyYbZ2tPQ4

crates/codegen/kigi-shell/src/session/storage/jsonl/tests.rs

@@ -2794,3 +2794,24 @@ async fn graph_mode_state_round_trips_and_tombstones() {
     let after = adapter.load_session_without_updates(&info).await.unwrap();
     assert!(after.graph_mode_state.is_none(), "cleared graph must not resurrect");
 }
+
+/// The barrier covers nested state files, and an unsyncable one fails it.
+#[cfg(unix)]
+#[tokio::test]
+async fn sync_session_files_reports_a_nested_file_that_cannot_be_synced() {
+    use std::os::unix::fs::PermissionsExt;
+    // Root opens anything; the permission probe is meaningless there.
+    if unsafe { libc::geteuid() } == 0 {
+        return;
+    }
+    let dir = TempDir::new().unwrap();
+    let adapter = JsonlStorageAdapter::with_explicit_session_dir(dir.path().to_path_buf());
+    let info = create_test_info();
+    adapter.init_session(&info, default_model_id()).await.unwrap();
+    let nested = adapter.goal_mode_state_file(&info);
+    std::fs::create_dir_all(nested.parent().unwrap()).unwrap();
+    std::fs::write(&nested, b"{}").unwrap();
+    std::fs::set_permissions(&nested, std::fs::Permissions::from_mode(0o000)).unwrap();
+    let error = adapter.sync_session_files(&info).await.unwrap_err();
+    assert_eq!(error.kind(), io::ErrorKind::PermissionDenied, "got {error}");
+}