the problem is with this step:

4. Prune empty containers.

you can prune/flatten these containers but then the deeper messages that you do have are not direct replies to their ancestors in the flattened/pruned version of the tree.

i didnt say that threading did not work. it does. but it is imperfect at best and can be misleading at worst.

in my case i was constructing an MPTT structure (Nested Set) for optimal thread fetching and simply leaving in the dummy message placeholders that i didnt have a copy of.

i plan to experiment further, but there arent really any earth-shaking revelations in that post. it's all fairly obvious.