remove a node

- associated links
- associated effects in effect list If effects are not used elsewhere
- node itself

No file paths or tests are referenced. Begin by inspecting the TypeScript source entry points to locate where node deletion is implemented and where links/effect state is stored. Then trace that flow to remove related links and only delete effects when they are not referenced by other nodes. Done means removing a node results in no orphaned links or effects remaining.

索引モデルが issue の本文から書いたものです。