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Method to investigate User Permissions?

I have a user in my team who seems to have lost permissions all of a sudden...

We use fork as a GIT UI and fork had "forgotten" about the previous installation/execution, so it went through user setup again and we had to select the appropriate SSH Key again.

We try to setup permissions via groups so it is surprising because other users don't seem to experience that problem.

I temporarily solved the problem by getting him to create a new SSH Key which I added at the Project level with read-write permissions.

It works but is excessive because I do not want him to have read-write on all repositories.

2 Questions:

1) What is the difference between declaring an SSH Key at the user account level rather than the project (or repository...)? Where could I find explanations about this?

2) Is there some kind of method I could follow to try to unravel his permission problems?

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