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I have several executable bin files in ~/bin and I want to launch them using the Gnome environment. For example, pressing the Super (Windows) key, typing the name in the search bar and then launch it.

How can I do this? What directory will Alt + F2 look for?

And are they (search bar and Alt + F2) the same one?

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They are not the same one.

The Alt-F2 prompt will autocomplete and execute anything that is in the PATH environment variable. This means that to be able to execute your files in ~/bin from there, you just need to set up the PATH variable in your ~/.bashrc file, adding the ~/bin path to it:

# just add this line to your bashrc

However, the search bar that you get when pressing Super is a completely different thing. To get an application showing up there you must add it to the menu, using the alacarte program, check out the explanation in this question: Adding custom applications to Gnome launcher

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