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Maybe one of the major problems facing all the a/c developments is the very long development cycle.
But I do question the need for a $$$$$ STOVL airplane given the ability to establish air dominance for virtually any theater of war we car imagine in the near future. Especially if that same airframe will sacrifice the ability to field other airframes or warfighter weapons due to budget constraints.
If any airplane were running Windows, it'd be in serious trouble. You don't use a consumer grade OS on a complex machine. Most likely it is a stripped down version of BSD or something similar. I would venture to guess it is some kind of hybrid UNIX OS that is set up with only the functionality it needs. THEN the software is developed for the needs of the aircraft.
Is there "out of the box" software for it? I doubt it. Besides, each generation of aircraft has newer and more complex systems that demand more programming and processing power.
Maybe a more modular approach to the software is the key. Once you have basic building blocks that all work, adding a module is less labor and time intensive.