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I found out that when I change directory with :cd, the root directory of NerdTree is not affected. How can I make NerdTree change its root when I use :cd?

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I believe your best bet is to utilize the command :NERDTreeCWD:

:NERDTreeCWD                                                      *:NERDTreeCWD*
    Change the NERDTree root to the current working directory.  If no
    NERDTree exists for this tab, a new one is opened.

Now you can't override :cd but you could create a custom command that's close...it just has to start with a capital letter:

:com! -nargs=1 -bar -complete=dir Cd :cd <args> | NERDTreeCWD

Use just like :cd...

:Cd /some/path

Never mind all that...this just occurred to me and is much better IMO.

There is an auto command event triggered by directory change

augroup DIRCHANGE
    au!
    autocmd DirChanged global :NERDTreeCWD
augroup END

That's it.

Note that this is only for the global directory change of :cd. To have this work with :lcd you'd change global to window or you could include both by separating them with commas. Full list:

"window"  to trigger on `:lcd`
"tabpage" to trigger on `:tcd`
"global"  to trigger on `:cd`
"auto"    to trigger on 'autochdir'.
"drop"    to trigger on editing a file
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    This is awesome. Thank you! Apr 23 at 4:40

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