feat: add phylogenetic analysis CLI command and lazy distance traits

Introduce the `obikphylo` crate to support genome-vs-genome distance matrix computation and phylogenetic tree inference via Neighbor-Joining and UPGMA algorithms. Extend the `obikmer2` CLI with a new `phylo` command that exposes configurable metrics, presence thresholds, and CSV/Newick output options. Refactor `obikindex` to expose trait-based partial aggregation for efficient distance metric finalization without full matrix materialization. Update dependency graphs and remove obsolete storage modules.

src/Cargo.lock

@@ -1677,6 +1677,7 @@ dependencies = [
  "obikindex",
  "obikindexer",
  "obikmerge",
+ "obikphylo",
  "obikquery",
  "obikrebuild",
  "obikrope",
@@ -1712,6 +1713,7 @@ dependencies = [
 name = "obikphylo"
 version = "0.1.0"
 dependencies = [
+ "kodama",
  "memmap2",
  "ndarray",
  "obicompactvec",
@@ -1725,8 +1727,10 @@ dependencies = [
  "obiskbuilder",
  "obiskio",
  "obisys",
+ "petgraph",
  "rand 0.10.2",
  "rayon",
+ "speedytree",
  "tempfile",
  "tracing",
  "tracing-subscriber",