This is the germ of what we know as the bonus.
For the game's first few years the ball did indeed stay in the basket after a successful shot, and someone had to climb a ladder or reach over a gymnasium balcony to retrieve it. Not until 1906 did the rules committee call for the removal of the bottom of the basket.
This is the original goaltending rule. The backboard would be introduced three years later, to protect spectators in balconies from the ball and to keep them from knocking the ball away from the basket.
In 1926 Naismith used adhesive, visible here, to mount the rules on cardboard with the intention of framing them for the wall of his office. But for some reason he never hung them, thereby keeping sunlight from damaging the document.
Naismith admitted he blew it with this rule, which touched off free-for-alls by granting possession to the first player to reach the ball after it went out-of-bounds. "One of the boys who played on an early team of mine takes great pleasure in exhibiting a scar that he got when he dived for the ball and came into contact with the sharp corner of a radiator," he once wrote. Not until 1902 would possession be awarded to the opponent of the last team to touch the ball inbounds. In the meantime, to deal with the mayhem spilling beyond the sidelines, gyms installed chicken wire around the court—which led to players being called cagers.
The five-second rule that we know today survives almost exactly as written here.
Naismith originally called for a strict division of labor between the game officials, with an umpire calling fouls and a referee tracking the ball. But this meant that guards, who usually played far from the umpire's station under the basket, could commit fouls with relative impunity. So the rules committee would gradually abolish distinctions between the officials.
Naismith often officiated; during his visit to Morningside College in Sioux City, Iowa, late in life, several students roped him into refereeing their pickup game without knowing who he was. "That old duffer never saw a game of basketball," one of them muttered. That night, at a banquet, this very player blushed deeply when he was introduced to the keynote speaker.
Today basketball has long since split into several branches—for high schools, colleges, men, women, pros and internationals—and length helps distinguish one set of rules from another: An NBA game lasts 48 minutes, a college or international game 40 and a high school game 32.
Naismith granted authority to the captains because he didn't foresee coaches in his new game. Basketball was invented to further the moral development of those who played it, and Naismith believed that the more decision making was left to the players, the better off they would be.