I have a command line app for this somewhere I wrote a few years back when I was commuting on Caltrain a lot, I should dig it up and publish it. It had some extra pathfinding/fuzzy search stuff. I almost always have my bike with me and I wanted to cover the edge cases where it's faster to bike to a nearby station to catch a bullet or where you can take a train the wrong direction a stop or two for the same purpose.

I wish there a maps app that would build entire itineraries taking into account that you have a bike with you, and ideally your average expected biking speed. It's so annoying to plan any sort of multi-transit itinerary in the bay, you always have to piece things together yourself or get stuck with some nonsense that takes 30% longer than it needs to.

Of course all of this could also be resolved if we had a sane transit system with short intervals.