AutoRefactor
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project specific clean options are stored in workspace preferences
The cleanup can be configured either in preferences or project specifically in the project properties of a java project. However, the enabled refactorings of the current cleanup profile are always stored in the global preferences, even when the profile is edited from project properties.
This can be a problem in team projects, where all editor cleanups, save actions, compiler settings etc. are stored as project properties in version control for full reproducability.