refactor: Shift KmerIndex ownership to Arc for thread-safe sharing

Replaces lifetime-bound references with runtime reference counting across multiple crates. This enables safe concurrent access across parallel workers without explicit cloning or manual lifetime management. Introduces the `query` and `utils` CLI commands in obikmer2, along with supporting modules for batch processing, sparse indexing, sliding-window findere logic, and output formatting. Updates dependency manifests and aligns test suites with the new ownership model.

src/obikdump/src/dump.rs

@@ -1,4 +1,5 @@
 use std::io::Write;
+use std::sync::Arc;
 use std::sync::atomic::{AtomicUsize, Ordering};
 
 use rayon::prelude::*;
@@ -39,7 +40,7 @@ pub trait IndexDump {
     ) -> OKIResult<()>;
 }
 
-impl IndexDump for KmerIndex {
+impl IndexDump for Arc<KmerIndex> {
     fn dump<W: Write, F: Fn() + Send + Sync>(
         &self,
         out: &mut W,
@@ -87,7 +88,7 @@ impl IndexDump for KmerIndex {
                         Ok(_)  => { write_row(buf, row, prefix); true }
                     }
                 };
-                let cache = IndexCache::new(self, Some(vec![i]));
+                let cache = IndexCache::new(Arc::clone(self), Some(vec![i]));
                 if debug {
                     cache.iter_partition_kmers_located(i, use_counts, n_genomes, filters, |part, layer, kmer, row| {
                         let seq = String::from_utf8(kmer.to_ascii()).unwrap_or_else(|_| "?".repeat(kmer_size));
@@ -106,7 +107,7 @@ impl IndexDump for KmerIndex {
             // ── Unbounded: no atomic, no contention ───────────────────────────
             (0..n).into_par_iter().map(|i| {
                 let mut buf = Vec::<u8>::new();
-                let cache = IndexCache::new(self, Some(vec![i]));
+                let cache = IndexCache::new(Arc::clone(self), Some(vec![i]));
                 if debug {
                     cache.iter_partition_kmers_located(i, use_counts, n_genomes, filters, |part, layer, kmer, row| {
                         let seq = String::from_utf8(kmer.to_ascii()).unwrap_or_else(|_| "?".repeat(kmer_size));

src/obikdump/src/unitig.rs

@@ -5,6 +5,7 @@
 //! foreign type, so this is an extension trait rather than an inherent `impl`.
 
 use std::io::Write;
+use std::sync::Arc;
 
 use obidebruinj::GraphDeBruijn;
 use obifastwrite::write_unitig;
@@ -25,7 +26,7 @@ pub trait IndexUnitigs {
     ) -> OKIResult<usize>;
 }
 
-impl IndexUnitigs for KmerIndex {
+impl IndexUnitigs for Arc<KmerIndex> {
     fn write_unitigs<W: Write + Send, F: Fn() + Send + Sync>(
         &self,
         out: &mut W,
@@ -40,7 +41,7 @@ impl IndexUnitigs for KmerIndex {
         let g = (0..n)
             .into_par_iter()
             .try_fold(GraphDeBruijn::new, |mut local_g, i| -> OKIResult<GraphDeBruijn> {
-                let cache = IndexCache::new(self, Some(vec![i]));
+                let cache = IndexCache::new(Arc::clone(self), Some(vec![i]));
                 cache.iter_partition_kmers(i, use_counts, n_genomes, filters, |kmer, _row| {
                     local_g.push(kmer);
                     true