Digging and more digging had turned the cramped backyard of a centuries-old North End home into a hole-pocked jumble of back-filled earth that most tourists passed without a glance on their way to Old North Church. But this blemish behind the 18th-century Clough House proved to be a blessing for archeologists, who say their dirty work this spring unearthed a rarely found time capsule from the neighborhood’s early days.