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the site is very old. version 3.3.0. I don't know if the libraries folder is ever supposed to have anything changed in it or if it would be safe to just delete that directory and upload a new libraries folder from a clean install of joomla of the same version.

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Hacked Joomla Sites: you can find many articles, posts and relevant documentation by searching in the web, including this site, regarding what you have to do to fix and secure your website.

Regarding the libraries folder: It's a folder where 3rd party extensions and developers may place files (scripts, libraries, frameworks etc). If you haven't add anything more than the core, then you could easily replace the whole folder. If you know that you have installed certain extensions that may have added additional files in the libraries, then re-installing them will install again those files.

Certainly you need to update to latest Joomla, as anything below 3.6.4 is vulnerable. Just do your homework and search for documentation as said above, in order to get a full list with tasks you have to do to clear and protect your site. Missing doing the recommended tasks, then likely your site will be hacked again in the next days.

Ask for professional help if you are unsure.

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Assuming core files have not been modified it should be safe to reinstall the Joomla files. Ideally, run a backup before you start in case anything goes wrong.

I highly recommend upgrading to the latest version of Joomla (currently 3.6.4) where the Joomla Update component has an option to reinstall core files (this feature was added around Joomla 3.6.0).

You could also use a commercial scanning tool that will tell you which files have been modified and offer to revert these to the original versions.

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