Trusted Files list will now fill with file entries by default. From CIS V5.4

The reason this will happen is explained in the quote below from Egemen

It is for optimization and faster operations guys. Embedded certificate verification takes too much time and once verification is done, the file is added to the trusted list for faster lookup in the future. It can handle millions of files with no problems. Hope this helps.

Mod Edit: Unless it is still unclear, safe files will be added to your Trusted Files list automatically. -HeffeD