For decades, the Petaluma River has been the lifeblood of Sonoma County's second-largest city. Once a haven for paddle-wheel steamers and barges transporting timber and bags of flour from the docks behind the Golden Eagle Mill (now the site of a busy shopping center) to San Francisco, this man-made slough has been sorely neglected in recent years, the source of costly flooding and a repository for pollutants. That could all change dramatically now that plans call for extensive development along its banks.