feat: add multi-genome SNP pseudo-alignment and CLI export

Introduces a `SnpAlignment` struct and helper methods to construct per-genome SNP pseudo-alignments from sibling k-mer data, filtering monomorphic families and encoding bases as IUPAC ambiguity codes. Exposes the type at the crate root for simplified imports. Adds a `--snp` CLI flag to compute and export these alignments as an IUPAC-coded FASTA file. Updates theory documentation to propose a multi-genome framing approach for joint phylogenetic inference, resolving pairwise correspondence ambiguities through positional homology and partial coverage thresholds. Bumps crate version to 1.1.40.

src/Cargo.lock

@@ -1715,7 +1715,7 @@ dependencies = [
 
 [[package]]
 name = "obikmer"
-version = "1.1.39"
+version = "1.1.40"
 dependencies = [
  "clap",
  "csv",