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/architecture/index.html

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-      <a href="../usage/reindex/" class="md-nav__link">
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@@ -1201,7 +1173,7 @@
 <li>Genome columns (count or presence data) are kept at a consistent width across every layer and partition after a merge, which is what allows whole-index aggregate distances (Jaccard, Bray-Curtis, Euclidean, Hellinger, …) to be computed as a two-pass cascade (local partial sums per partition, then a global combination) with no double counting.</li>
 </ul>
 <h2 id="parallel-execution-and-numa-awareness">Parallel execution and NUMA awareness</h2>
-<p>Partition-level work (index construction, <code>merge</code>, <code>filter</code>, <code>reindex</code>, <code>select</code>, <code>phylo</code>'s sibling-annex/Sankoff computations) is dispatched by a partition runner that adapts to the machine's memory topology, detected automatically at startup via hwloc:</p>
+<p>Partition-level work (index construction, <code>merge</code>, <code>filter</code>, <code>convert</code>, <code>select</code>, <code>phylo</code>'s sibling-annex/Sankoff computations) is dispatched by a partition runner that adapts to the machine's memory topology, detected automatically at startup via hwloc:</p>
 <ul>
 <li>On a multi-socket / multi-NUMA-node machine, one thread pool is pinned per NUMA node, and each partition is processed entirely by threads pinned to one node — keeping the memory a partition touches local to that node's DRAM. This matters because touching kmer data across NUMA nodes without pinning can degrade throughput by an order of magnitude or more on large multi-socket machines.</li>
 <li>On a single-socket machine, Apple Silicon, or if hwloc cannot report NUMA topology, all cores are treated as one node with no pinning and negligible overhead — this is the default behavior on macOS.</li>