diff --git a/.codegraph/.gitignore b/.codegraph/.gitignore
index d20c0fe..5d41e6a 100644
--- a/.codegraph/.gitignore
+++ b/.codegraph/.gitignore
@@ -1,5 +1,13 @@
 # CodeGraph data files — local to each machine, not for committing.
-# Ignore everything in .codegraph/ except this file itself, so transient
-# files (the database, daemon.pid, sockets, logs) never show up in git.
+# Ignore everything in .codegraph/ except this file itself. Known transients:
+# SQLite database and WAL/SHM, daemon.pid, sockets, and logs. The catch-all
+# covers anything codegraph init adds later.
+codegraph.db
+codegraph.db-wal
+codegraph.db-shm
+codegraph.db-journal
+daemon.pid
+*.sock
+*.log
 *
 !.gitignore
diff --git a/.gitignore b/.gitignore
index a8afdd8..63ee3c0 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,8 @@
 agent-squad
 agent-squad-data/
 *.test
+
+# CodeGraph local index. A second layer so the database stays untracked even
+# if .codegraph/.gitignore is overwritten by codegraph init.
+.codegraph/*
+!.codegraph/.gitignore
diff --git a/Agent-Native b/Agent-Native
index 5a998b3..49e6dd1 160000
--- a/Agent-Native
+++ b/Agent-Native
@@ -1 +1 @@
-Subproject commit 5a998b3609a1ed8749371b26adba751082eb9096
+Subproject commit 49e6dd1e0fc65de7f259f21d2f63c56e5b165a48
diff --git a/README.md b/README.md
index 40e8640..7361d0d 100644
--- a/README.md
+++ b/README.md
@@ -178,6 +178,10 @@ go build -o agent-squad .
 ./agent-squad serve --addr :8090       # ③ HTTP API（REST + SSE）
 ```
 
+## CodeGraph
+
+`codegraph init` 的索引写在 `.codegraph/`。仓库只跟踪 `.codegraph/.gitignore`。SQLite 数据库、WAL、pid、socket 和日志留在本机；根目录 `.gitignore` 与该文件双重忽略，避免索引被提交。
+
 ## 验证
 
 ```bash