Well, you can disable window controls in gnome and KDE afaik if you want. Then you'll only have the various app-specific buttons that are necessary for functionality.
If you're looking for every app to have a vim-like interface or something, well, that seems a bit unrelated to CSDs.
That's a good tip - so far what I've done is I have this note in Zotero of "Things to enter into bibliography".
The way I keep track of information source is that every sentence I write has atleast one source. This is probably a bad way to do things as I now have 180 footnotes and I'm not nearly done with the first decade.