I have on several sites hundreds (or thousands) of modified files.
I will reset everything to zero, trying to think the next time I'm doing update to do the same thing.
The most would be not to make those false positives that affect 99% of my file changes. I make some changes manually but I will identify them quickly.
Will you soon implement this feature (already spoken) to be more zen !!
In the next version (3.1.6) I will add a first step identifying extensions updated/added although new/modified files will still be shown. I'm not sure if finally the file integrity will not show those files as implementing this feature is not as easy as I thought.
Take note that the file integrity alerts were designed to tell you "Ey, some files have been modified", so marking all files as "safe" should be done with no fear if you launched an update or installed a new extension.
The problem in disabling en masse is that it can still have a real alert
If 100 ~ 200 files are changed in the minute, it seems unlikely that it is a hacker so it would be visible !!, but I will look at the next version with attention.
Other ideas: to distinguish additions from modifications? indicate version number of the extension?
The problem here is to identify if the modified file belongs to any of those extensions installed/updated. There are packages, components, plugins and modules and not all developers use descriptive names to be fully sure that a file belong to an installed extension. This is why currently I can't exclude modified files: I don't want to lose a real alert.
Anyway take note that all files reported by the file integrity are automatically scanned by the malware scanner, so if there is a threat you will be inmediately notified.