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I like to have two or three vertical windows with code and a NERDTree to the left, among other things. From any of these windows I'd like to instantly jump to the NERDTree window, and when I choose to edit a file, I'd like that file to show up in the window I was in.

Are these things possible with the current state of the NERDTree plugin? It seems to me that :NERDTreeToggle is supposed to do the first thing I ask for according to the help, but no matter how I open a file, it always shows up in the window right next to my NERDTree.

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Try :NERDTreeFocus to jump to the NERDTree window from any open window. This was added relatively recently, it seems:

https://github.com/scrooloose/nerdtree/pull/132

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