Apparently the problem is with the tracks being on the sand - things have moved. Better article than the one Bob listed actually tries to explain what's going on: [
www.sandiegouniontribune.com]
Apparently some freight is getting through on slow order. Passenger service is completely stopped. Amtrak may start running bus bridges between Irvine and Oceanside next Monday; two trainsets are apparently trapped in San Diego.
Bob: your 1980 San Clemente project was updated for one of the LOSSAN plans in the 1990s or early aughts, I think. Why has it never gone anywhere? The one I remember seeing was generally located along I-5, partly in tunnel, and in large part doable with cut & cover work. So it's kind of a longer version of the Del Mar tunnel scheme, but with a station in the middle someplace.