I had a look around there yesterday on my way to Willits; according to a sign posted by the site, this is flood-control work being done by the Army Corps of Engineers. They seem to be replacing the NWP Petaluma Creek bridge just north of the depot (behind Longs), and have removed the P&SR bridge at the end of Copeland Street (behind Petaluma Trolley's yard). Since the feed mill had been reached by crossing the P&SR bridge, they are putting in a lead directly from the NWP main. This seems like a case of building new trackage specifically because the old trackage was removed to further the Corps project--I suspect it doesn't necessarily mean that trackage will ever actually be used (although I hope it does). Lots of nice new ties and pretty heavy rail going into it, anyway.
When the new 880 freeway was built through West Oakland to replaced the collapsed Cypress structure, the SP got lots of new first-rate trackage out of the deal. To this day, there are a goodly number of switches and pieces of trackage in Emeryville and West Oakland that have never been used.