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There is a strange situation in which the sync info for a folder is lost. It involves a Java Project that contains a bin folder that is shared but empty. I suspect what is happening is that the bin folder is pruned on checkout and then created by the builder. Because of this, the sync info is not properly restored from the phantom.
Should investigate for RC3 since it is reproducable
The problem is that the project is not mapped to the provider when the checkout occurs (i.e. the project is mapped after the checkout completes) so the delta listeners for CVS skip the deltas for the project. This makes the problem a bit too complicated to consider for 2.1. Moving to 2.2.
This was fixed in 3.0 M9