I just noticed that with ArcGIS Pro 3.0, there is yet another system folder in ArcGIS Pro project folders, namely GPMessages. There are the following system folders in my brand new project and I believe there are even more out there once you start using it:
- .backups
- GPMessages
- ImportLog
- Index
My suggestion is to combine all of those folders into a single folder. They're a nuisance when it comes to source control and you have to make exceptions for every new folder that pops up when you use a project and perform an action. I have to put the projects I used for publishing into source control. Also, it's annoying to look into a project folder and half of the items are something I don't care about.