I want to write an application (C# would be best, other are also welcome) that works in the background in Windows/Linux, but is able to put characters in inputs and textareas of currently active window, in applications like Notepad, Browser URL Address and so on. How is this possible?
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Take a look at the SendKeys class. This should handle your situation.
Edit: If you want a Java solution, take a look at the Robot class.