What is the Automatic WordPress File Scanner and how does it work?

The Automatic WordPress File Scanner is a part of the Hack Guard module. It scans and monitors WordPress files for changes. 
It automatically scans the integrity, detects and repairs your core WordPress folders, plugin & theme files and PHP malware.
This is a single filesystem scanner, which is a combination of the 4 scanners:
The setting can be found under the Config menu > Scanners:

When it runs, it’ll run all the available scanners together in 1 single pass, including any extras we add further down the line.

The scanner also tightly integrates with our ShieldNET Hashes API, meaning results are far more accurate, especially for premium plugins and themes.

To learn how to configure this scanner and how it works in practice, we highly recommend you to read A Complete Guide To The Shield Security Scans here.