I recommend SlowQuitApps: github.com/dteoh/SlowQuitApps it shows a loading bar when you hit Command + Q, giving you time to think if you really want to close the app.
Another mention goes to Marta marta.yanex.org/, an alternative to Finder or TotalCommander.
For the command line I'd recommend mac-cli or m-cli for doing tasks with the console like restarting, locking, changing volume and so on.
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