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commented
1 month ago @JamesLee-Jones This reworking turned out to be reasonably straightforward, so - assuming that this solves the problems that you and @JonathanFoo0523 encountered - I think it's better to go this route rather than trying to upstream work-arounds to protobufs.
To avoid a restriction of the protobuf library that limits the recursion depth of a protobuf message, this change reworks the way the mutation tree is represented in protobuf format. The tree is now organised as a flat list of nodes, and the children of a node are identified via indices into this list.
Fixes #192.