feat: Implement query subcommand for sequence-to-genome mapping

This change introduces the `query` CLI command and its supporting infrastructure for sequence-to-genome mapping and k-mer matching. It adds a `QueryLayer` abstraction backed by MPHF and persistent matrices, exposes the index partition for direct querying, and implements `Hash`/`Eq` for `RoutableSuperKmer`. The command ingests sequence batches, deduplicates superkmers, routes them to index partitions for parallel exact or 1-mismatch matching, and outputs results as FASTA records annotated with JSON metadata. Includes `serde_json` dependency addition, module exports, and documentation updates.

src/obikindex/src/index.rs

@@ -185,6 +185,11 @@ impl KmerIndex {
         Ok(())
     }
 
+    /// Borrow the inner partition for direct superkmer-level queries.
+    pub fn partition(&self) -> &KmerPartition {
+        &self.partition
+    }
+
     /// Path to the unitigs file for partition `part`, layer `layer`.
     pub fn layer_unitigs_path(&self, part: usize, layer: usize) -> PathBuf {
         self.partition.part_dir(part)