Two years after its launch as a new online news organization covering the San Francisco region, the Bay Citizen is reconsidering its mission and editorial focus under new management. As of May 1, it merged operations with the Berkeley-based Center for Investigative Reporting, one of the granddaddies of the nonprofit news world, and ended its editorial partnership with the New York Times. The combined newsroom now marshals a staff of 70 and an annual budget of $11 million for news reporting from the San Francisco Bay Area. But differences between the news organizations’ editorial priorities and funding structures point to many challenges ahead, according to journalists from both the Bay Citizen and CIR. The Bay Citizen, which was founded and launched in 2010 by the late San Francisco philanthropist Warren Hellman, focused on timely news about Bay Area communities and tried to compete with other local news outlets to break stories.