feat: enable index resumption and enforce directory creation

The command now supports reopening existing indexes instead of failing when the output file exists. Control flow branches between opening an existing index and constructing a new one, moving configuration setup exclusively to the creation path. Directory existence is enforced upfront with proper I/O error propagation. The --force flag retains its original semantics by removing the target directory before proceeding with a fresh build.

DevDoc/theory/evolutionary_distances/index.html

@@ -1244,14 +1244,14 @@
   
   
     <li class="md-nav__item">
-      <a href="../../implementation/obilayeredmap/" class="md-nav__link">
+      <a href="../../implementation/layer_tier/" class="md-nav__link">
         
   
   
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-    obilayeredmap crate
+    obikindex layer tier
   
 
     
@@ -1489,6 +1489,34 @@
 
               
             
+              
+                
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+  
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+  
+    <li class="md-nav__item">
+      <a href="../../implementation/partition_layer_cache/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Partition and layer caching (discussion)
+  
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+    
+  </span>
+  
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+      </a>
+    </li>
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@@ -3582,7 +3610,7 @@ diagonal entry directly, at no extra lookup cost.</p>
 <p>Mirror <code>distance.rs</code>: open the presence or count store per partition. But
 instead of a per-partition <code>partial_*</code>, run the sequential source sweep:</p>
 <div class="highlight"><pre><span></span><code>for p in 0..n_partitions:                       # OUTER — sequential
-    open source partition p&#39;s layers (QueryLayer-style, obikpartitionner)
+    open source partition p&#39;s layers (QueryLayer-style, obikindex::partition)
     enumerate distinct canonical k-mers of p (one per MPHF slot) with their
         presence/count vectors                   # column-major, as query stage 2
     par_iter over these source k-mers:           # INNER — rayon, thread-local tally
@@ -3605,7 +3633,7 @@ instead of a per-partition <code>partial_*</code>, run the sequential source swe
     merge thread-local tallies into global SnpTally
 </code></pre></div>
 <p>The inner lookup is precisely <code>QueryLayer::find_slot</code> +
-<code>col_value(g, slot)</code> (<code>obikpartitionner/src/query_layer.rs</code>) — reuse or factor
+<code>col_value(g, slot)</code> (<code>obikindex/src/partition/query_layer.rs</code>) — reuse or factor
 out that path rather than reimplementing MPHF access. Enumerating "all distinct
 k-mers of a partition with their vectors" is the <code>dump</code>/<code>query</code> stage-2
 column-major scan already implemented in <code>dump_layer.rs</code> /