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For example, the system knows that if I press Ctrl+B inside this textarea of Ask Question the web browser will handle it in some way (format text as bold), and if I press Alt+Tab it will be handled by GNOME (switch active window), etc.

How can I know all the assigned keyboard shortcuts and their functions at anytime in Ubuntu? Is there any tool that enumerates/monitors/scans such keyboard shortcuts?

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By "system" I figure you mean the user interface. There is no simple answer to your question. Every single event (as they are called in programming lingo) be it a key pressed or a drag-and-drop move has been dealt with programmatically by some piece of code in the program you are currently using.

To learn more you have to read some book on UI frameworks for linux (GTK is used by Gnome, QT is used by KDE). Basically, the UI framework provides a signal/slot mechanism to handle events(signals being fired by events and slots being program code to take appropriate action).

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