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SAN FRANCISCO — Microsoft’s cloud computing deal with Oracle was some two years in the making — going from careful negotiations over just the terms of the meetings themselves to a more open and fluid relationship between executives at the two longtime rivals.

Windows Azure GM Steven Martin

“When it comes to working together on cloud, it was actually pretty easy,” said Steven Martin, the Windows Azure general manager who drove the deal for Microsoft. “We said, ‘We want to work together in a way that works for you, that works for our customers, and works for us. We’re not looking to do anything to try to … ”

“Go through your garbage?” I interjected during an interview with Martin yesterday, referring to Oracle’s infamous hiring of professional investigators who attempted to purchase a Microsoft advocacy group’s trash from a janitorial service.

“… change your dynamics, or pick through your trash,” continued Martin. “It’s just not like that. Customers want and expect to run Oracle workloads in the cloud. We’d sure like to help make that happen.”

Who made the first overture? Oracle or Microsoft?

“I would say it was joint,” said Martin. “We’ve been working back and forth for a long time as (Oracle CEO Larry Ellison) has considered different options for how they approach cloud.”

Martin said he had been working on the partnership for the last two years, but seriously for the last year, and most intensively over the past six months.

How do the Oracle and Microsoft cultures fit together?

“Better than you might think,” said Martin. “When we’re able to go back and talk about things in terms of first principles, we want customers to have a great experience.

“When customers are running an Oracle workload in a Windows Server environment, or running it in Azure, we expect that to be a good experience for them. That means licensing, that means pricing, that means customer support. Let’s just do this right. There’s no point in attempting to hold the ocean back with a broom. The world is going to cloud. Let’s do this together and be smart about it.”

It also may have helped that Martin himself has deep connections to Silicon Valley, as a veteran of companies including Netscape who spent time working on Linux and contributed to other open-source projects. He’s an example of Microsoft’s broadening of its own leadership in recent years.

The deal between Microsoft and Oracle, announced earlier this week, will let corporate customers run Oracle software on Microsoft’s Windows Azure cloud computing platform and Hyper-V virtualization technology.

It also officially brings the Java programming language to Azure. The companies say they will “work together to add properly licensed, and fully supported Java into Windows Azure – improving flexibility and choice for millions of Java developers and their applications.”

It’s one of a series of agreements made this week between Oracle and competitors including

Microsoft’s Martin made the comments during a wide-ranging, behind-the-scenes interview about Windows Azure at the company’s Build conference in San Francisco yesterday. Microsoft is trying to compete more effectively with Amazon Web Services in the market for cloud computing.

On stage earlier in the day, the company had brought out Aaron Levie, the CEO of file-storage company Box, a Microsoft competitor, to promote the upcoming ability for Windows Azure to connect to a variety of online services for single sign-on inside companies.

“It’s really exciting to see an all-new Microsoft,” Levie said on stage.

Martin pointed to the company’s support of Linux in Windows Azure, the Oracle announcement, and an announcement this week with Engine Yard as continued evidence of Microsoft’s new ways.

“Now with Box up on stage, I think the Valley is running out of things to complain about,” he said. “We’ve really shown how open we are and how seriously we’re taking it.”

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