docs: document k-mer index architecture and refactor distance metrics

Add comprehensive documentation for the `obilayeredmap` crate, `PersistentCompactIntVec`, `PersistentBitVec`, and the hierarchical k-mer index architecture, including sidebar navigation updates across all documentation pages. Refactor the Bray-Curtis distance computation in `obicompactvec` to decouple numerator and denominator calculations, replacing direct pairwise calls with explicit loops over precomputed sums. Update tests to verify column sum accuracy and align with the simplified API.

doc/implementation/chunkreader/index.html

@@ -347,6 +347,42 @@
   
 
     
+  </span>
+</a>
+</li>
+<li class="md-nav__item">
+<a class="md-nav__link" href="../obilayeredmap/">
+<span class="md-ellipsis">
+    
+  
+    obilayeredmap crate
+  
+
+    
+  </span>
+</a>
+</li>
+<li class="md-nav__item">
+<a class="md-nav__link" href="../persistent_compact_int_vec/">
+<span class="md-ellipsis">
+    
+  
+    PersistentCompactIntVec
+  
+
+    
+  </span>
+</a>
+</li>
+<li class="md-nav__item">
+<a class="md-nav__link" href="../persistent_bit_vec/">
+<span class="md-ellipsis">
+    
+  
+    PersistentBitVec
+  
+
+    
   </span>
 </a>
 </li>
@@ -385,6 +421,18 @@
   
 
     
+  </span>
+</a>
+</li>
+<li class="md-nav__item">
+<a class="md-nav__link" href="../../architecture/index_architecture/">
+<span class="md-ellipsis">
+    
+  
+    Kmer index
+  
+
+    
   </span>
 </a>
 </li>