storage: fix PT updates in case of late AnswerUnfinishedTransactions
This is done by moving self.replicator.populate() after the switch to MasterOperationHandler, so that the latter is not delayed. This change comes with some refactoring of the main loop, to clean up app.checker and app.replicator properly (like app.tm). Another option could have been to process notifications with the last handler, instead of the first one. But if possible, cleaning up the whole code to not delay handlers anymore looks the best option.
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