Ignore CodeGraph indexes from the repository root as well.

A second ignore layer keeps the SQLite database local even if codegraph init overwrites the nested policy file. Pin Agent-Native to the same policy.

Co-authored-by: Cursor <cursoragent@cursor.com>

.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
+# Ignore everything in .codegraph/ except this file itself. Known transients:
-# files (the database, daemon.pid, sockets, logs) never show up in git.
+# 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

.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

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