"So I'd like to know if navigation/organisation of the forum will be changed to the way it was before. If yes, when will this happen?"
In a sense, yes the organization of the forum will come back. Type in "ethics" for example, and you will have all of the ethics threads listed. Type in "philosophy of religion" and you will have all of those threads listed. We have a lot of work to do though on the organizational aspect of the forum.
Now, what we need to do as a community is organize the forums by using descriptive tagging. Let's say you make a thread that raises an ethical concerns about factory farms. For tags, you would probably want to use "philosophy," "ethics," "animals," "factory farms," "agriculture," or other such related tags so that not only the correct audience can find the thread, but so that random searches will reveal related topics quickly and efficently.