Ensure `agglo.Rag.separate_fragments` leaves a consistent graph

[jni]

Currently, the separate_fragments methods splits up the merge tree, but it doesn't touch the graph. This means that the merge tree and the graph are inconsistent with each other and results in later errors.

Two things need to happen:

• when splitting off two branches of the tree, the implied RAG nodes need to be built.
• one of the two branches needs to be merged to the parent of the deleted node, if applicable.