refactor: extract index construction state tracking into extension trait

Moves pipeline state bookkeeping, including sentinel file marking and spectrum persistence, into the algorithms' run and close methods. Introduces a crate-private extension trait to satisfy Rust's orphan rule while implementing construction-only operations on KmerIndex. Updates helper function visibility for cross-crate access and removes the now-empty index_layer module.

src/Cargo.lock

@@ -1563,6 +1563,7 @@ dependencies = [
  "memmap2",
  "niffler",
  "obicompactvec",
+ "obidebruinj",
  "obikindex",
  "obikrope",
  "obikseq",