The university has recoiled at some of the sweeping changes the Trump administration demanded. Harvard’s president, Dr. Alan M. Garber, has singled out several as intrusive and unconstitutional, including demands that might influence whom the university hires and admits. With billions of dollars in research funds in jeopardy, the university’s leaders are now negotiating with the White House. But an eventual deal may not fully capture the changes, small and large, already enacted at Harvard before any papers are signed. Early in the spring, an aggressive and polarizing new presidential administration drafted a menu of demands, many of them very...