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SF has plenty of money for transportation. It's just used very ineffectively.

Citation needed. :-) Is the money used on the wrong things? Or on the right things, but not efficiently? Many public works projects end up over budget and behind schedule, so I guess that should be factored in.

Where is the money going, and/or where should it be going?

What % of people who work in San Francisco also live there?

San Francisco's budget is vastly less efficient than other comparable US cities:

http://www.sfweekly.com/sanfrancisco/the-worst-run-big-city-...

As for people living vs. working in SF, this comment does an excellent job explaining it, with sources:

https://news.ycombinator.com/item?id=10875936

tl;dr: The increase in population due to daily workers commuting in from outside is vastly smaller than in NYC.

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