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Removing generated classes from output directory doesn't trigger automatic rebuild. I'm not sure if this is intended or not, but Project->Build Project menu entry is disabled when automatic rebuilding is enabled so I suppose it's not intended behavior. However if current behavior is correct then I suggest to enable Project->Build Project and Project->Build All menu entries so that there is an intuitive way to trigger rebuild manually. Workaround is to clean the project, but it may not be obvious, especially for less experienced users.
As far as I know, the output folder is not supposed to be managed by the user. The builder is responsible of putting files there. Kent any comment?
Why are you removing .class files?
Our release script did it, which I ran by accident. It was obviously my fault but the point is, I believe there should be an obvious way of fixing such situation or detect it and fix automatically.
The obvious way is to clean the project so its rebuilt. We are looking into some automated detection, but that is being tracked in bug 99497 *** This bug has been marked as a duplicate of 99497 ***
*** Bug 112053 has been marked as a duplicate of this bug. ***