chore: update ci cache, document distance metrics, and bump version

Updated CI workflow cache keys with a `v2` salt and `Cargo.lock` hash to prevent stale incremental compilation caches and deadlocks, while updating restore keys and documenting interrupted job state. Introduced a 3-way ordinal distance metric framework that replaces ambiguous IUPAC encoding with explicit k-mer scoring, bridging pairwise methods to character-based phylogenetics via Sankoff parsimony. Bumped the `obikmer` crate version to 1.1.42.

src/Cargo.lock

@@ -1715,7 +1715,7 @@ dependencies = [
 
 [[package]]
 name = "obikmer"
-version = "1.1.41"
+version = "1.1.42"
 dependencies = [
  "clap",
  "csv",

src/obikmer/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "obikmer"
-version = "1.1.41"
+version = "1.1.42"
 edition = "2024"
 
 [[bin]]