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Update documentation for CLI command renames and new commands

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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.
This commit is contained in:
Eric Coissac
2026-08-28 23:06:05 +02:00
parent 95fa0c93b2
commit caf59b5658
38 changed files with 666 additions and 2433 deletions
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mkdocs-user.yml
+1 -2
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@@ -46,10 +46,9 @@ nav:
- dump: usage/dump.md
- annotate: usage/annotate.md
- phylo: usage/phylo.md
- name-tree: usage/name-tree.md
- unitig: usage/unitig.md
- estimate: usage/estimate.md
- reindex: usage/reindex.md
- convert: usage/convert.md
- utils: usage/utils.md
- pack: usage/pack.md
- Predicates and taxonomy paths: usage/predicates.md