Neovim Indent Bug?

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I have the following options in my .config/nvim/init.vim:

set tabstop=4
set shiftwidth=4
set expandtab
set ai
set smartindent
filetype on
filetype plugin on
filetype indent on

So, the indentation engine should work on all files, but it does not. When I edit my config file for example, :set ai returns: autoindent and :set si returns: smartindent. But when I run the same commands on a php file they return:

noautoindent
nosmartindent

EDIT: The file that was overriding my config is: /usr/share/nvim/runtime/indent/php.vim It's the default php indent file.

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