Malicious code on the site, how to detect?

Question

Computer networks

Yandex.Webmaster detected malicious code on the site, and the site is displayed as potentially dangerous in search results. To search for and identify specific files with viruses, I used Kaspersky, SUPERAntiSpyware, Malwarebytes Anti-Malware, AVG, AVZ, Avast! and others, nothing malicious was found. Then I tried the Manul utility recommended by Yandex to check on the server side. About 600 suspicious files were found, but the problem is that the "suspicious" list includes CMS system files and jquery-type scripts that do not contain malicious code (I manually checked and re-uploaded some, but the result did not change). Advise how to find and cure files containing malicious code, what software products to use?

Answer 1

Git/Mercurial, for the future.