A marathon negotiating session between a major San Francisco Bay Area transit agency and its two largest unions ran well into a second day Thursday as both sides worked toward a deal to end the months-long contract dispute that has left many riders under the repeated threat of a commute-crippling strike.A marathon negotiating session between a major San Francisco Bay Area transit agency and its two largest unions ran well into a second day Thursday as both sides worked toward a deal to end the months-long contract dispute that has left many riders under the repeated threat of a commute-crippling strike.