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Case 1. Let's set the pref to _not_ prune empty dirs. Create a project with two folders, F1 and F2. Create a file in F1. PPP -> Team -> Share Project. In the Synchronize view, add the project to version control. Note that it prunes F2 in the sync view. No commit the whole project. In the Navigator, the project is still dirty, and shows F2 not being under version control. If we now manually say F2 -> Add to version control, and even commit the whole project, it's still dirty.
Case 2. If the prune pref is "DO prune", it does not change the behavior.
It turns out that the error in case 1 existed in 2.0.2. Strangely, the error in case 2 does not occur when you are debugging (making in difficult to track down). We'll add this bug to the readme for 2.1.
We have spent some time investigating it some more with JML, and we observed some additional subtleties. 1. The bug happens only for first-time added folders on a new project. That is, you reproduce the bug as described above, and then make "update". The project is clean, and *from that point on*, it looks like the bug can't be reproduced - adding new folders behaves fine. 2. The bug is very sensitive to the order of operations. If we add the empty folder to verson control directly from the navigator - without first adding the whole project _using the sync view_, the project gets marked as clean. JML and I both believe this bug is not for 2.1.
I would amplify statement (1) in the last comment. It turns out even just creating and adding a new empty folder permanently rectifies the problem.
This bug has not been touched for 2 years. Closing as WONTFIX. Please reopen if you feel this is still an important issue.
