I'm not convinced that the difference between a singly rooted tree and a multiple-rooted tree is going to make that much difference. I mean, think about it... if you 100k's or even millions of files, is anybody going to parse through all of that, looking for a reusable function, even if it is on their workstation?

And sure a compiled language would catch naming collisions on functions or whatever, but nothing stops somebody from creating a method

doQuickSort( ... )

and somebody else creating

quickSortFoo(...)

where they are semantically equivalent (or very nearly so).

It seems to me that the problem of duplicating code, because you don't know that a method already exists to do what you're trying to do, is the same problem regardless of how your tree is laid out; and is ultimately more of a documentation / process / discipline issue. But I'd be curious to hear the counter-argument to that...