Hi, I have the same question and I have tried a couple of ways to deal with it. My conclusion is that it is a bad idea to exclude the PBL's when using GIT since you want to have a complete and fully functional copy of your development folders on the remote GIT repository if you have to pull the project to a new computer or another folder. So you shouldn't put the *.pbl in the .gitignore file.
If you want to ignore files created when deploying an application, just put *.pbd, *.dll, *.exe and maybe som more filters in the .gitignore file. The .gitignore file must be in the root folder and in my case this is the same folder as my workspace file.
For some reason the PBL's are marked as modified when doing anything with the objects inside a PBL. And I found out that it's better to leave them and not push them to the remote repository since you will get an error that the local PBL file can't be merged with the server version. Probably since the PBL is a binary file.
Yes, it's annoying and makes the list of changed files messy when using any external GIT client. It would be nice to be able to use filter in the list of changed files in the GIT client. Unfortunately this doesn't seem to be possible in GitKraken or Sourcetree.
/Fredrik