feat: introduce genome metadata tracking and CSV export

This commit replaces raw string genome labels with a structured `GenomeInfo` type for better metadata tracking. It adds a `--meta` flag to the index command, and implements a new `annotate` CLI subcommand to import metadata from CSV files or export it via `--dump`. Distance and shared-count matrices are now serialized to CSV, with UPGMA clustering trees exported as Newick files. Query outputs now include per-genome k-mer match counts in JSON, while fixing syntax and variable naming issues in index merging and dump generation.

src/Cargo.lock

@@ -601,6 +601,27 @@ dependencies = [
  "typenum",
 ]
 
+[[package]]
+name = "csv"
+version = "1.4.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "52cd9d68cf7efc6ddfaaee42e7288d3a99d613d4b50f76ce9827ae0c6e14f938"
+dependencies = [
+ "csv-core",
+ "itoa",
+ "ryu",
+ "serde_core",
+]
+
+[[package]]
+name = "csv-core"
+version = "0.1.13"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "704a3c26996a80471189265814dbc2c257598b96b8a7feae2d31ace646bb9782"
+dependencies = [
+ "memchr",
+]
+
 [[package]]
 name = "cvt"
 version = "0.1.2"
@@ -1500,6 +1521,7 @@ name = "obikmer"
 version = "0.1.0"
 dependencies = [
  "clap",
+ "csv",
  "indicatif",
  "kodama",
  "obifastwrite",
@@ -2192,6 +2214,12 @@ version = "1.0.22"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "b39cdef0fa800fc44525c84ccb54a029961a8215f9619753635a9c0d2538d46d"
 
+[[package]]
+name = "ryu"
+version = "1.0.23"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "9774ba4a74de5f7b1c1451ed6cd5285a32eddb5cccb8cc655a4e50009e06477f"
+
 [[package]]
 name = "same-file"
 version = "1.0.6"