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The day before his Watergate pardon was announced, Richard Nixon telephoned President Gerald Ford and threatened that unless it was granted he would claim publicly that Ford ''had promised the pardon in exchange for the presidency.'' This is what reporter Seymour Hersh contends in the latest issue of The Atlantic Monthly. The report says the alleged phone call was made Sept. 7, 1974, as a lawyer representing Mr. Ford was negotiating with Mr. Nixon and his representatives on conditions under which a pardon would be granted. Ford has repeatedly denied making such a bargain before Nixon's resignation.