The $100 million real estate deal that led to the Barclays Center being built over a century-old rail yard is beginning to pay dividends for the Long Island Rail Road and its Brooklyn commuters, officials said.

Seven years into the construction of a state-of-the-art new storage facility to replace the original Vanderbilt Yards, workers will soon punch through a 171-year-old rail tunnel to provide trains, for the first time, a direct path between the yard and Atlantic Terminal.

It's one of many improvements to the LIRR's Brooklyn operation that are being delivered to the railroad free of charge by Greenland Forest City Partners, a joint venture between Greenland and Forest City Ratner, developer of the Barclays Center and adjacent Pacific Park residential project.

"A project like this has to be a win-win for everybody," said Ratner vice president Thomas Bonacuso, who heads the project. "Brooklyn has become a brand. Brooklyn is hot. We and the railroad capitalized on that and were able to bring improvements to their rail yard that wouldn't have been possible under their own resources."

For decades, all LIRR trains terminating in Brooklyn have had to double-back east about a half-mile into the Atlantic Avenue rail tunnel, come to a complete stop, and then return west to access the rail yard, where they are serviced and stored before being put back into service.

The process blocks other trains from using the tunnel for six to eight minutes at a time -- totaling about two hours a day, officials said. And so when the LIRR entered into negotiations with Ratner more than a decade ago to sell the air rights to Vanderbilt Yards, it made the creation of a new West Portal -- and other improvements -- a condition of the deal.

"The completion of the new yard with the West Portal will, of course, bring an end to any behind-the-scenes issues in the operation of the train yard," LIRR spokesman Salvatore Arena said. "The LIRR will reap the operational benefits of a state-of-the-art train storage and maintenance facility, constructed at no cost to the railroad."

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Those upgrades include new electric signals to replace antiquated manual signals, and sewer connections on all nine yard tracks to service bathrooms on the train. Most trains could only have their toilets pumped at one track in the original yard.

Ratner officials declined to disclose the project's cost. The new yard is expected to be finished in December 2017, after which Greenland Forest City Partners will build a platform on top of the yard that will provide LIRR trains, and workers, shelter from the elements, and serve as the foundation for several new apartment buildings.

Ratner executive vice president Robert Sanna said the project's location has been "a blessing and a curse."

"The blessing is they're sitting on a transportation hub. The curse is they're sitting on a transportation hub," Sanna said. "It just makes the construction that [much] more complicated, because it has to be dealt with in a way that keeps the transportation always in service."

Wayne Bailey wishes the developer and the LIRR would give nearby residents as much consideration as it has given commuters. Bailey, who says he lives less than 20 yards from the project site, said keeping trains running during the project has required a lot of the construction to take place on nights and weekends.

"There are as many floodlights on as there are during most baseball pitches," Bailey said. "It is problematic. . . . We would love to have it built and done with as soon as humanly possible."

Completion of the project will also help the LIRR carry out its plan to eventually replace regular scheduled Brooklyn service with "scoot" shuttle trains between Atlantic Terminal and Jamaica.

While the LIRR says the plan will increase the number of trains into and out of Atlantic Terminal, it will require all Brooklyn riders to transfer at a dedicated platform at Jamaica.

"While there are some benefits . . . we want to make sure everybody benefits from it," Commuter Council chairman Mark Epstein said.