Something that could work with git is to use a map.

Transform:

    (a1 a2 (b1 b2))

To:

    -------------
    parent  child
    -------------
    root    list1
    list1   a1
    list1   a2
    list1   list2
    list2   b1
    list2   b2

It should work with diff too if the ids are preserved.