Fix all test failures from bd-166 (missing issue_prefix)

Completed bd-167: Fixed all tests that failed with 'database not initialized: issue_prefix config is missing' error.

Changes:
- Created test helper functions in 3 locations:
  * cmd/bd/test_helpers_test.go (already existed)
  * internal/rpc/test_helpers.go (new)
  * internal/storage/sqlite/test_helpers.go (new)

- Updated all affected test files to use newTestStore():
  * cmd/bd: comments, export, git_sync, label, list, reopen, direct_mode
  * internal/rpc: rpc_test, version_test
  * internal/storage/sqlite: sqlite_test, underlying_db_test

- Fixed config test: updated flush-debounce default from 5s to 30s

- Removed unused sqlite imports from test files

All tests now passing ✅

Also:
- Closed bd-167, bd-170 (cleanup of beads-* duplicates)
- Removed corrupt backup files

Amp-Thread-ID: https://ampcode.com/threads/T-4a8c6002-9384-45b6-81f6-2907d1e4c6c2
Co-authored-by: Amp <amp@ampcode.com>

cmd/bd/export_test.go

@@ -8,7 +8,6 @@ import (
 	"path/filepath"
 	"testing"
 
-	"github.com/steveyegge/beads/internal/storage/sqlite"
 	"github.com/steveyegge/beads/internal/types"
 )
 
@@ -22,10 +21,7 @@ func TestExportCommand(t *testing.T) {
 	defer os.RemoveAll(tmpDir)
 
 	testDB := filepath.Join(tmpDir, "test.db")
-	s, err := sqlite.New(testDB)
-	if err != nil {
-		t.Fatalf("Failed to create store: %v", err)
-	}
+	s := newTestStore(t, testDB)
 	defer s.Close()
 
 	ctx := context.Background()
@@ -228,10 +224,7 @@ func TestExportCommand(t *testing.T) {
 
 		// Create empty database
 		emptyDBPath := filepath.Join(tmpDir, "empty.db")
-		emptyStore, err := sqlite.New(emptyDBPath)
-		if err != nil {
-			t.Fatalf("Failed to create empty store: %v", err)
-		}
+		emptyStore := newTestStore(t, emptyDBPath)
 		defer emptyStore.Close()
 
 		// Test using exportToJSONLWithStore directly (daemon code path)