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Synchronization has two parts (in most of the VCS) -- updating the working copy of data to reflect the most recent state in the repository, and vice-versa, committing all changes made in the local working copy to the repository. These two operations will be presented separately, not as one "synchronization" operation. Both should be executable on the whole project (distinguishing the project contents and project settings), whole Portfolio and on selected objects in the project files view. Conflicts during synchronization due to concurrent changes are reported to the user to resolve. From the user perspective, adding and removing objects is expected to be done automatically within the 'commit' operation. This is however not the way the VCS systems work. A special support for comfortable commit is needed to be designed and implemented. However this is highly desirable, it is not planned for the first release at the moment. The user will have to perform VCS 'add' and 'remove' operations explicitly on individual objects. That should be possible both in the project files view.
Reassigning vcscore issues to versioncontrol->vcscore.