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Arabic, Jewish, Continental Philosophy
(I'm going through the recent JHPs and seeing what categorization puzzles arise.)

I would be inclined to put Arabic philosophy in with the rest of the Western tradition.  Medieval Islamic philosophy works with the same ancient texts as medieval European philosophy, works with most of the same problems, and are discussed in the Christian tradition.  There doesn't seem to be anywhere else to put it, also.

There is a  category under 'Other Philosophical Traditions' entitled European Philosophy, Misc. It includes Judaic philosophy and recent Continental, but there are already places to put Maimonides and recent Continental figures in the History of Western Philosophy branch.  I guess these are for non-historical Jewish and Continental papers, but you ought to make a decision about when history begins and mere dispute starts.  Moreover, some of the 'Other Traditions' include non-western traditions under which historical papers would have to be placed (e.g. Chinese philosophy).

May I suggest that you start history relatively late (e.g. 20 years before present)?  Also, let me suggest that 'Other Philosophical Traditions' restricted to non-western philosophy, both historical and recent.  Let History of Western Philosophy include Jewish, Islamic, Iberian, and Eastern European philosophies. Let commentaries on Heidegger, Derrida, and Foucault all go in the relevant cubbyholes in the history of Western.   Let recent non-historical phenomenology find a place in the philosophy of mind.  Let distinctively Jewish, non-historical recent philosophy find a place in philosophy of religion.  And so on. 

I see that there are hard problems here, but everything in history should be able to find one and only place between History of Western and Other Philosophical Traditions.

Arabic, Jewish, Continental Philosophy
There are really two distinct issues here.  First, whether papers in these traditions should be included in the history tree (and in the topic-based trees).  Second, whether we should have categories for these traditions under "Other Philosophical Traditions".

I'm inclined to think that the answer to the first question, the answer to the second question should be yes.  It's just useful to have a place where papers in these traditions are gathered together.  Someone working in Continental philosophy or in Arabic philosophy will presumably appreciate having one place to go, organized by the principles inherent to these traditions rather than by others' principles.

Of course a yes answer to the second question doesn't preclude a yes answer to the first question.  It's already the case that we intend papers classified in the OPT tree to also be classified in the topic-based trees where relevant.  And as you note, many papers in Continental philosophy already have a place in the history tree (although clearly this doesn't apply to non-historical Continental papers).

So the main question is whether we should treat Arabic/Islamic, Judaic philosophy, and Misc European philosophy in the same way that we're already treating Continental philosophy, by including figures from these traditions in the history tree as well.  This might well make sense, especially as the tree is labeled "history of Western philosophy".  Of course we can have a fair amount of crosslisting of categories between the history tree and the OPT tree.

Arabic, Jewish, Continental Philosophy
Here again, the merits of cross-classification dawn on me slowly.
Still, I can't help but think that the present versions of the fourth and fifth categories is unduly kludgy.  You say "Continental philosophy or in Arabic philosophy will presumably appreciate having one place to go, organized by the principles inherent to these traditions rather than by others' principles,"  but now you organize 17th/18th by time, then place, then name.  Presumably, the organization of Arabic philosophy won't be much more sophisticated.

Let me suggest that the organizing principle of the fourth category be: time then place.  And the organizing principle of the fifth category be: place then time.  Everything in the fourth category could then find its place in the fifth (automatically, perhaps).  The fifth category could contain, in addition, current approaches to such and such (Jewish philosophy, Continental).  There's no reason for the fourth category to be restricted to the history of just the west.  There will be lots of gaps, and where there is no philosopher, you don't need a category.  Still, this system will make things more intuitive for the categorizer and for the user.

A few caveats: I use 'place' a little loosely.  Sometimes it would be better to replace that with religious categories.  Averroes and Maimonides were both born in Spain, but its better to count them as Arabic (or Islamic) and Jewish than as Iberian.  Likewise with early Analytic and Continental (which aren't religious categories, but aren't exactly geographical categories, either).

And, in the twentieth century, there are more names, and the categories should sometimes go two deep before getting to names.   This is sort of a null case, and the fifth category classifications of Continental philosophy (for example) can be carried over cleanly to the corresponding branch of the fourth category.  (Aside from the impersonal 'Current Approaches to Continental'.)