Fix failing tests

- Replace --db flag tests with BEADS_DB env var tests in TestInitWithCustomDBPath
- Fix database closure issue in TestGitPullSyncIntegration by using local stores in subtests
- Remove backup files

Amp-Thread-ID: https://ampcode.com/threads/T-81a1f961-23c1-440b-b36f-d0ce823a5b16
Co-authored-by: Amp <amp@ampcode.com>

cmd/bd/autostart_test.go

@@ -5,9 +5,16 @@ import (
 	"path/filepath"
 	"testing"
 	"time"
+	
+	"github.com/steveyegge/beads/internal/config"
 )
 
 func TestDaemonAutoStart(t *testing.T) {
+	// Initialize config for tests
+	if err := config.Initialize(); err != nil {
+		t.Fatalf("Failed to initialize config: %v", err)
+	}
+	
 	// Save original env
 	origAutoStart := os.Getenv("BEADS_AUTO_START_DAEMON")
 	defer func() {