fix(graph): remove the database sidecars when clearing checkpoints

- SQLite keeps committed state in -wal and -shm beside the database

tests/test_checkpoint_lifecycle.py

@@ -153,3 +153,20 @@ def test_cli_style_usage_saves_then_resumes():
 
         # Cleared on success -> a later run starts fresh.
         assert checkpoint_step(tmp, "AAPL", "2026-05-08", sig) is None
+
+
+@pytest.mark.unit
+def test_clearing_removes_the_database_sidecars(tmp_path):
+    """SQLite writes -wal and -shm next to the database; leaving them behind
+    means a cleared checkpoint still has committed state on disk."""
+    from tradingagents.graph.checkpointer import clear_all_checkpoints
+
+    cp = tmp_path / "checkpoints"
+    cp.mkdir(parents=True)
+    for suffix in (".db", ".db-wal", ".db-shm"):
+        (cp / f"NVDA{suffix}").write_text("x")
+
+    cleared = clear_all_checkpoints(str(tmp_path))
+
+    assert cleared == 1
+    assert list(cp.iterdir()) == []

tradingagents/graph/checkpointer.py

@@ -71,13 +71,19 @@ def checkpoint_step(data_dir: str | Path, ticker: str, date: str, signature: str
 
 
 def clear_all_checkpoints(data_dir: str | Path) -> int:
-    """Remove all checkpoint DBs. Returns number of files deleted."""
+    """Remove all checkpoint databases. Returns the number of databases deleted.
+
+    SQLite keeps committed state in ``-wal`` and ``-shm`` files beside the
+    database, so deleting only the ``.db`` leaves a cleared checkpoint with data
+    still on disk.
+    """
     cp_dir = Path(data_dir) / "checkpoints"
     if not cp_dir.exists():
         return 0
     dbs = list(cp_dir.glob("*.db"))
     for db in dbs:
-        db.unlink()
+        for path in (db, *cp_dir.glob(f"{db.name}-*")):
+            path.unlink(missing_ok=True)
     return len(dbs)