Ctrl-V (or, again, sometimes Ctrl-Shift-V in a terminal) pastes the clipboard buffer. Middle mouse button (or shift-Insert) pastes the selection buffer.
Is there still room for confusion?
Also there are some cases where javascript which selects text for you causes very unintuitive behavior wrt selection buffer.
I don't have a problem with X selection+paste if I'm just using Linux. But using it when connected to a remote machine via various remoting technologies (NX, Chrome Remote Desktop), and then mix in that the host machine is a Mac with its terrible command/control split, and the result is pretty confusing.
Vim and emacs also have their own shortcuts for accessing the clipboard buffer.
But as far as I can tell, if text is selected for you that's not always true. I sometimes have difficulty with text boxes which insist on self-selecting as soon as I click them, and which I just can't seem to pull into the selection buffer.
Github doesn't seem to have this issue, but I had recently when trying to get a google maps permalink, for example.
Combined with xdg-open, I clone the repos locally just clicking the 'Clone' link.
http://i.imgur.com/AiTFm2R.png
Userscript itself in: https://github.com/kidd/org-protocol-github-lines/blob/clone...
[1] http://www.nongnu.org/autocutsel/
[2] Sample .zshrc to map edit-command-line to Ctrl-x e:
edit: fixed shortcut for bashedit: forgot about my .zshrc