Months after allegations of financial mismanagement at the Berkeley Divinity School first surfaced, Berkeley and the Yale Divinity School signed a reaffiliation agreement yesterday.

While most of the terms of the contract remained the same, the new agreement states more emphatically that all financial transactions must go through Yale systems.

“It makes clear that all money has to flow through the Yale system, which was one of the things that wasn’t being done,” said Worth Loomis ’45, the vice chairman of the Berkeley Board of Trustees. “The old agreement called for that also, but it’s more explicit in this one.”

Yale President Richard Levin said little has changed from the old contract, but added that the new one does contain “modest revisions.”

“It clarified numerous features of the relationship,” Levin said. “In particular, it clarified the budgetary control of the University and the role of the University in the appointment, reappointment and dismissal of the dean.”

Sources from Berkeley and Yale have both said for weeks that they have been close to finishing the agreement but were trying to work out a few last details.

“It wasn’t really a disagreement in substance; it was a question in wording,” Levin said.

Berkeley, an Episcopal seminary affiliated with the Yale Divinity School, has been at the center of a controversy since December.

The Hartford Courant reported in December that a Yale-initiated confidential audit found that then-Dean R. William Franklin had improperly spent school money on his daughter’s Harvard Medical School tuition and other personal expenses. Franklin resigned on Jan. 1.

Christian R. Sonne, who is the chairman of Berkeley’s Board of Trustees, told the Yale Daily News in late January that he supported Franklin’s request for a $10,000 tuition payment but was unaware that such a payment violated University policy.

Berkeley Treasurer John Sargent is now receiving training in University accounting procedures.

The Rev. Frederick Borsch has accepted a position as interim dean, but the school is also currently conducting a search process to find a permanent replacement for Franklin.

“Berkeley is very fortunate to have attracted [Borsch] as the interim dean,” Levin said. “He is an outstanding scholar and leader in the Episcopal church and we are just delighted to have him here at Yale for the months ahead.”

While Berkeley has finalized its relationship with the University, it still faces an ongoing investigation by the state Attorney General’s Office.