Ok, so I ran a couple of tests, I removed the
sonar.projectBaseDirfrom the xml file and ran with 9.0.1 and 9.0.2. Both work as expected.
Hey @fbraun4358 , thanks for the confirmation that it worked.
From what I can tell, this solves your issue, as you were trying to set the projectBaseDir to the current working directory, which was the default behavior with or without the flag.
You are right that relative paths are not respected, and I understand it is frustrating that the hotfix release broke your previous behavior. The main point was that it never worked, but there was another issue were the projectBaseDir was calculated ONLY from the CLI parameters, ignoring the global file. So by fixing one issue, this one came up 
.
I made a ticket in our backlog to track this, but since you can keep working without the property at all, if you don’t see any other problems, feel free to mark this as the solution.