The quote is contrasting the summer session with the regular school year at Devon.
During the summer session, the student body "had been an idiosyncratic, leaderless band...undirected except by the eccentric notions of Phineas." Because of the smaller numbers ("a few dozen boys"), all were housed in close proximity to each other; because of the lack of other students who were interested in serving as organizers and leaders of student government, Finny became the unofficial leader and originator of ideas and activities.
Now, with the beginning of the "one hundred and sixty-third Winter Session," the seven hundred boys who made up the usual student body of Devon School were back on campus and settling into their regular patterns. Leper no longer lived in the suite across the hall from the room shared by Gene and Finny during the summer session; Brinker Hadley, the dedicated student politician who revelled in his role of leadership in the student government, had taken occupancy of that suite and was already meeting with others who were interested in getting the year's business items under way. Leper was no longer included in the mainstream of activities, but "had been moved to a room lost in an old building off somewhere in the trees toward the gym."
The quote is contrasting the carefree and peaceful summer session with the business-like hustle of the regular school year.