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If someone is able to upload a webshell he will be able to upload hundred of them because there will not be an attack. The atacker will use the file directly, so there is no query for Joomla and no Web Application Firewall (Joomla based) will be able to detect it.
1 / looking at the pirate's files, how do you think it's gone if it's not by the site ?
The malware scanner can be launched:
2 / normally the scanner should have detected it? not sure that the knowledge base was the last, because not sure updates via the control center
If you have a backup (do you have akeeba, don't you?) just use Akeeba kickstart and you will have your site online in a few minutes.
3 / for the reinstallation of the sit, are my steps correct :