Update documentation for CLI command renames and new commands

Renames the reindex command to convert across all usage guides and navigation menus. Adds documentation for the newly introduced name-tree command. Updates flag references, such as replacing --metric with --distance in pack and phylo modules, and adjusts MkDocs configuration to match the revised structure. All changes are strictly limited to documentation and configuration files.
2026-08-28 23:06:05 +02:00
parent 95fa0c93b2
commit caf59b5658
38 changed files with 666 additions and 2433 deletions
@@ -790,34 +790,6 @@
  
  
  
-    <li class="md-nav__item">
-      <a href="../../usage/name-tree/" class="md-nav__link">
-        
-  
-  
-  <span class="md-ellipsis">
-    
-  
-    name-tree
-  
-
-    
-  </span>
-  
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-              
-                
-  
-  
-  
-  
    <li class="md-nav__item">
      <a href="../../usage/unitig/" class="md-nav__link">
        
@@ -875,14 +847,14 @@
  
  
    <li class="md-nav__item">
-      <a href="../../usage/reindex/" class="md-nav__link">
+      <a href="../../usage/convert/" class="md-nav__link">
        
  
  
  <span class="md-ellipsis">
    
  
-    reindex
+    convert