A secret Apple warehouse is on land the government wants for a new Silicon Valley train station

It's no secret that Apple is expanding rapidly in Silicon Valley, because it needs more space to house its rapidly growing workforce working on research and development, possibly for the long-rumored Apple Car.

One of its new secret facilities is a former FedEx distribution center in Santa Clara that Apple leased last year. It's codenamed "Magnolia."

Turns out, that warehouse could become part of a eminent domain fight, reports Nathan Donato-Weinstein for the Silicon Valley Business Journal. Various government bodies believe that specific location is necessary for building BART Silicon Valley, an extension of the light rail system that will eventually connect San Francisco and San Jose.

Construction on the BART extension is expected to start in 2018. An official for the Santa Clara Valley Transportation Authority told the Business Journal that "it's a bump we're going to have to negotiate."

The BART tracks won't run directly through the site, but plans from 2007 indicate that it's important for staging construction materials. Other plans, according to the report, indicate that it could be a transit hub with a "mixed-use village that drives mass transit ridership" including both a BART station and a Caltrain station.

Valley Transportation Authority documents from 2007 describe a 12-acre station where the Apple facility currently stands.

If government were to decide to take the eminent domain route, it could be expensive. Although Apple doesn't own the site, it's reportedly entered into a long-term lease and has started to spend millions to improve the location, including installing an "regenerative thermal oxidizer" and other industrial tools.

Permits filed last summer show that Apple plans to run a "Cathode/Anode Operation" out of the site.

Apple has said that it supports commuting alternatives to cars, and has a 34% participation goal for public transport participation at its new "spaceship" headquarters. The new Cupertino campus will have a "mass transit shuttle link" that transports employees to BART, Caltrain, and other light rail stops.