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.

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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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doc/usage/convert/index.html

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