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I cannot reproduce this with a local CVS on a linux machine. These are the steps I took:
Create new project
Enter CVS information
Checkout a Submodule from CVS
initial scan after checkout
removed files from CVS with eclipse client
update in Jabylon
After that, the removed files have been removed properly from the UI.
It's possible the problem is caused by the different path syntax on windows, but that's hard to test here.
Check if the diff listener does get notified about deletes and remove these properties.
We should check how Git behaves here
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