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/obikstats/src/stats.rs

@@ -1,5 +1,6 @@
 use std::fs;
 use std::path::Path;
+use std::sync::Arc;
 
 use rayon::prelude::*;
 
@@ -88,22 +89,22 @@ fn layer_bytes(layer: &KmerLayer) -> LayerBytes {
 /// once up front — this is diagnostic tooling, not a hot path, so trading
 /// that eager open for not having to hand-reconstruct every layer's file
 /// paths is the right tradeoff here.
-pub struct BitsPerKmer<'a> {
-    index: &'a KmerIndex,
+pub struct BitsPerKmer {
+    index: Arc<KmerIndex>,
 }
 
-impl<'a> BitsPerKmer<'a> {
-    pub fn new(index: &'a KmerIndex) -> Self {
+impl BitsPerKmer {
+    pub fn new(index: Arc<KmerIndex>) -> Self {
         Self { index }
     }
 }
 
-impl Algorithm for BitsPerKmer<'_> {
+impl Algorithm for BitsPerKmer {
     type Output = IndexBitsPerKmer;
 
     fn run(&mut self) -> obikalgorithm::Result<IndexBitsPerKmer> {
         let n_genomes = self.index.meta().genomes()?.len().max(1);
-        let cache = IndexCache::new(self.index, None);
+        let cache = IndexCache::new(Arc::clone(&self.index), None);
         let layers: Vec<&KmerLayer> = cache.iter().collect();
 
         let (n_kmers, mphf_b, evidence_b, matrix_b) = layers
@@ -148,23 +149,23 @@ impl Algorithm for BitsPerKmer<'_> {
 /// genome has a non-zero value (presence = 1, count > 0) — via
 /// `KmerLayer::col_weights` (`obicompactvec::ColumnWeights`), one call per
 /// layer instead of hand-opening each layer's matrix and summing rows.
-pub struct GenomeKmerCounts<'a> {
-    index: &'a KmerIndex,
+pub struct GenomeKmerCounts {
+    index: Arc<KmerIndex>,
 }
 
-impl<'a> GenomeKmerCounts<'a> {
-    pub fn new(index: &'a KmerIndex) -> Self {
+impl GenomeKmerCounts {
+    pub fn new(index: Arc<KmerIndex>) -> Self {
         Self { index }
     }
 }
 
-impl Algorithm for GenomeKmerCounts<'_> {
+impl Algorithm for GenomeKmerCounts {
     /// `(total_distinct_kmers, per_genome_kmer_counts)`.
     type Output = (usize, Vec<u64>);
 
     fn run(&mut self) -> obikalgorithm::Result<(usize, Vec<u64>)> {
         let n_genomes = self.index.meta().genomes()?.len();
-        let cache = IndexCache::new(self.index, None);
+        let cache = IndexCache::new(Arc::clone(&self.index), None);
         let layers: Vec<&KmerLayer> = cache.iter().collect();
 
         let total_kmers: usize = layers.iter().map(|l| l.n()).sum();