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How in the heck whether software is closed or open sourced make a difference when run in Linux?
It is a lot more easier, less expensive and less cumbersome to manage open source software in Linux than closed source. Qt realizes that. Real Network does too. Nvidia even had to provide open source wrappers to link their modules to Linux.
Will the OS give me a warning telling me that what I am about to run is closed source?
No, it doesn't. I don't see why it should. However, installing, maintaining and upgrading it will one make your life as a user hard.e.g the need to recompile the nvidia driver everytime I upgrade my kernel.
Just because the OS itself is open source, doesnt mean that it was meant to run only open source programs.
In many instances, it does. You can't link proprietary modules to many parts of the Linux kernel, for instance. In several cases proprietary applications can't link to free/open libraries on your system. They need to write their own.
Writing closed software is not impossible, it's just hard. And that's because like I said, the system is inherently designed to thrive in an free/open source atmosphere. Much of these is delibrate by design.