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/test_helpers_test.go

@@ -2,6 +2,8 @@ package main
 
 import (
 	"context"
+	"os"
+	"path/filepath"
 	"testing"
 
 	"github.com/steveyegge/beads/internal/storage/sqlite"
@@ -12,6 +14,10 @@ import (
 func newTestStore(t *testing.T, dbPath string) *sqlite.SQLiteStorage {
 	t.Helper()
 	
+	if err := os.MkdirAll(filepath.Dir(dbPath), 0755); err != nil {
+		t.Fatalf("Failed to create database directory: %v", err)
+	}
+	
 	store, err := sqlite.New(dbPath)
 	if err != nil {
 		t.Fatalf("Failed to create test database: %v", err)
@@ -19,10 +25,42 @@ func newTestStore(t *testing.T, dbPath string) *sqlite.SQLiteStorage {
 	
 	// CRITICAL (bd-166): Set issue_prefix to prevent "database not initialized" errors
 	ctx := context.Background()
-	if err := store.SetConfig(ctx, "issue_prefix", "bd"); err != nil {
+	if err := store.SetConfig(ctx, "issue_prefix", "test"); err != nil {
 		store.Close()
 		t.Fatalf("Failed to set issue_prefix: %v", err)
 	}
 	
+	t.Cleanup(func() { store.Close() })
 	return store
 }
+
+// newTestStoreWithPrefix creates a SQLite store with custom issue_prefix configured
+func newTestStoreWithPrefix(t *testing.T, dbPath string, prefix string) *sqlite.SQLiteStorage {
+	t.Helper()
+	
+	if err := os.MkdirAll(filepath.Dir(dbPath), 0755); err != nil {
+		t.Fatalf("Failed to create database directory: %v", err)
+	}
+	
+	store, err := sqlite.New(dbPath)
+	if err != nil {
+		t.Fatalf("Failed to create test database: %v", err)
+	}
+	
+	// CRITICAL (bd-166): Set issue_prefix to prevent "database not initialized" errors
+	ctx := context.Background()
+	if err := store.SetConfig(ctx, "issue_prefix", prefix); err != nil {
+		store.Close()
+		t.Fatalf("Failed to set issue_prefix: %v", err)
+	}
+	
+	t.Cleanup(func() { store.Close() })
+	return store
+}
+
+// openExistingTestDB opens an existing database without modifying it.
+// Used in tests where the database was already created by the code under test.
+func openExistingTestDB(t *testing.T, dbPath string) (*sqlite.SQLiteStorage, error) {
+	t.Helper()
+	return sqlite.New(dbPath)
+}