Can I build an OS with Gdevelop? How do you do it?
No you cannot. An operating system is by definition software that manages computer hardware, software resources. GDevelop games are built to be run managed by an OS, not to manage resources and hardware by themselves 
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While you cannot build a whole OS, you could still build a shell.
GDevelop could help creating an application that runs on the OS, it could present itself similar to an Android Home Screen, a Windows Desktop or …
This sounds a bit odd, but your applications would be GDevelop-created games or other websites and you have a nice graphical portal to choose from.
It is possible in more detail, I do not really understand how to do this, how can I find out which applications the user has installed, because all of them have different.
Assuming you are not trying to build an operating system but more of like a shell.
Have you had a look how today’s shells are organized? Such as Windows desktop (which essentially is Explorer), or a Gnome desktop?
When applications are installed the desktop environment needs to be informed about it so it will create a menu entry or an icon the user can click. If that does not happen, users can still run such applications by opening a generic ‘run’ window and typing the command themselves.
So you can definitely start off with a configuration file that contains a list of all applications for the shell. In the beginning you have to fill the data manually, but eventually the installation procedure could add entries right after having installed a new application.