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The big question with this is how to decide when to do it...

Maybe:

1) Determine the relative location of the source to the
project file.
2) Start with the designated obj directory. (If there isn't
one, forget the whole thing.)
3) For each component in the relative path found in (1)
where a corresponding directory exists in the current
location, move the current location into that directory. If
the corresponding directory does not exist, ignore that path
component.

With this scheme the developer can seperate the obj files to
any degree desired by precreating the required directory tree.