In reply to Aliv Faizal Muhammad.

If you are super security focused I have a foolproof method:

ssh into your server as root, and runchattr -R +i public_html/

This changes all file and directory file attributes to immutable, meaning the files cannot be changed, added to, or deleted. Since pretty much all exploits rely on the ability to add or modify files on your server its pretty effective. When you want to run plugin or core updates you just have to shell in and remove the attribute.

chattr -R -i public_html/