Use Sets to track atom relationships

[tim-smart]

Summary

• replace array-backed Atom parent and child relationships with Sets
• preserve parent-child links when a derived Atom reads the same parent more than once
• add the v4 regression test adapted to the v3 Registry API
• include a patch changeset for @effect-atom/atom

Why

Relationship updates previously performed linear scans and swap-pop bookkeeping. Duplicate parent entries could also cause a still-active relationship to be removed during dependency reconciliation.

Validation

• pnpm test --run (102 tests passed)
• pnpm lint
• pnpm check

Closes EFF-228