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For disabling X11 middle click paste, I found an interesting SO post but the best answer I saw and tested myself and it works, was the one by Suraj Inamdar about one third of the way down the page:

https://unix.stackexchange.com/questions/24330/how-can-i-tur...

What sucks is I use middle click paste all the time so now I'll have to decide if I want to leave it disabled for potentially improving security.

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That removes your middle mouse button entirely! (Unreliably due to the use of numbers with xinput, which can change; xinput can take names to avoid that issue). The issue will remain if the primary selection is pasted into a terminal by other means (personally, I use a key combination rather than mouse button) and won't be an issue if clipboard.autocopy is set to false in about:config in Firefox (per torgard's comment).

I've also set dom.event.clipboardevents.enabled to false since I don't want websites messing with the clipboard.

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