The Bay Citizen and the Center for Investigative Reporting, two non-profit organizations based in the Bay Area, announced formally Tuesday that they intend to merge. Under terms of the agreement, Berkeley, Calif.-based CIR, which also runs California Watch, would take over management of the Bay Citizen, an online publication with a publishing partnership with The New York Times. Phil Bronstein, a former Hearst executive and chairman of CIR's board of directors, will become the executive chairman of the combined companies, the two organizations said in the announcement. The rest of the…