I don't think this makes large repos fundamentally hard. You just need good support for working on incomplete graphs. For example you just need to know the tree

I don't think this makes large repos fundamentally hard. You just need good support for working on incomplete graphs. For example you just need to know the tree IDs/hashes of the non-checked-out trees in the directories that you have checked out. Then you graft your checked out directories onto the tree of the parent.