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I find myself opening files inside the wrong window in Vim -- sometimes the NERDTree or MiniBuffExplorer -- and it's really throwing me off.

I'm sure it's happening because my cursor is mistakenly focused inside one of these windows, but is there anything I can add to my vimrc to prevent this from happening?

A: 

It's possibly related to the setting of mousefocus. From :help mousefocus

The window that the mouse pointer is on is automatically activated. When changing the window layout or window focus in another way, the mouse pointer is moved to the window with keyboard focus. Off is the default because it makes using the pull down menus a little goofy, as a pointer transit may activate a window unintentionally.

rlduffy