message: refactor: revert "make usage of sets consistent to clarify intent"
  reverts commit
  This transformation is not correct and fails unit tests.
diff: @@ -45,7 +45,7 @@ export function findPrivateMutations(node: AuspiceTreeNodeExtended, seq: Analysi
  // This is effectively a set difference operation
  seq.substitutions.forEach((qmut) => {
  - if (!(node.substitutions?.has(qmut.pos) && node.substitutions?.get(qmut.pos) === qmut.queryNuc)) {
  + if (!(node.mutations?.has(qmut.pos) && node.mutations?.get(qmut.pos) === qmut.queryNuc)) {
  privateMutations.push(qmut)
  }
  })
  