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1. Constructor should not mention DataObject, there is no need for it. 2. handleXXX methods can show dialogs? Does that mean that they are called from AWT thread or from safe thread where they can block for result of AWT operation? - need more threading info.
ad 1. infrastructure needs to know the .project file, in fact it is identification of the project. (e.g. when IDE is closed and restarted, infrastructure has to find .project file and reread it again in order to preserve list of open projects) ad 2. this is bug IMO, operation shouldn't block calling thread, it can be replanned to AWT or any other 'safe' thread. handleXXX methods are just notifications, e.g. when handleModification is called the project is loaded and working already, thus we can wait for user's response without blocking caller of this method.
Fixed. Dispatched dialog code to the event thread, and updated javadoc for the handleXXX methods to state that the method can be called from any thread. I have not addressed issue #1 since Vita said it's necessary and you haven't disputed that; if you disagree reopen the bug.
Silence means agreement.
As described in http://www.netbeans.org/servlets/ReadMsg?msgId=619519&listName=nbdiscuss the current work on projects prototype has been stopped. Marking issue as CLOSED.