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.

doc/usage/unitig/index.html

@@ -9,7 +9,7 @@
       
       
       
-        <link rel="prev" href="../name-tree/">
+        <link rel="prev" href="../phylo/">
       
       
         <link rel="next" href="../estimate/">
@@ -702,34 +702,6 @@
                 
   
   
-  
-  
-    <li class="md-nav__item">
-      <a href="../name-tree/" class="md-nav__link">
-        
-  
-  
-  <span class="md-ellipsis">
-    
-  
-    name-tree
-  
-
-    
-  </span>
-  
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-              
-                
-  
-  
     
   
   
@@ -858,14 +830,14 @@
   
   
     <li class="md-nav__item">
-      <a href="../reindex/" class="md-nav__link">
+      <a href="../convert/" class="md-nav__link">
         
   
   
   <span class="md-ellipsis">
     
   
-    reindex
+    convert