I'd venture to say that if you're using a Vim plugin, you're going to want hidden files shown by default, especially considering you need to edit your .vimrc and use git.
It could optionally be set in your .vimrc to show or hide hidden files by default. Maybe there's a way to do this already?
It looks like you could put 'let g:NERDTreeShowHidden=1' (without the quotes) in your ~/.vimrc. See the doc for more info: https://github.com/scrooloose/nerdtree/blob/master/doc/NERD_tree.txt#L647
Thanks. I just think that the scenarios in which you _wouldn't_ want to see hidden files are edge cases. Just my opinion though.
One argument is that it follows ls's semantics (but then why I as the shortcut?).
It looks like this issue has been resolved. Generally, most people don't want to see the hidden files by default, but I'm glad you found the setting to use in these cases.
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It looks like you could put 'let g:NERDTreeShowHidden=1' (without the quotes) in your ~/.vimrc. See the doc for more info: https://github.com/scrooloose/nerdtree/blob/master/doc/NERD_tree.txt#L647