You have two choices
1. You keep a common large merged tree. Scalability arguments I think
are wrong here. They make assumptions inconsistent with the growth
in computing power, in memory, in disk and in networking.
2. You keep everything in pieces. If you do this your project flies
apart and you spend your entire life glueing it back together, and
failing probably to succeed.
A large merged tree does not mean you always have to download it all, it does
not mean you have to set interfaces in stone either. The perl folks manage
to do pretty much the same thing. Im sure we can
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