Environment
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CloudBees CI (CloudBees Core) on modern cloud platforms - Managed controller
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CloudBees CI (CloudBees Core) on traditional platforms - Client controller
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CloudBees Jenkins Enterprise - Managed controller
Resolution
If your build uses some Java based build tools (for example Gradle) they might be storing some information in the HOME directory. If the agent user does not have a HOME directory, Java Runtime might return the ? instead of the path. Hence, the new directory named ? is created in the current directory which is by default the workspace.
Make sure that the agent user has a HOME directory and then re-launch the agent.
Workaround
Tools might accept an override for the user home directory. For example, in case of Gradle you can use the GRADLE_USER_HOME environment variable to specify the Gradle user home directory (which defaults to $USER_HOME/.gradle if not set).