Eric Coissac dd889854cb rename distance subcommand to phylo ...

Rename the distance CLI subcommand to phylo across the codebase, documentation, and build configurations. Relocate source files from cmd/distance/ to a dedicated cmd/phylo/ module, update all internal routing references, and adjust benchmark scripts and Makefile targets to reflect the new command name.

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..

annotate.md

docs: add obikmer user guide and MkDocs build configuration

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dump.md

docs: add obikmer user guide and MkDocs build configuration

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estimate.md

docs: add obikmer user guide and MkDocs build configuration

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filter.md

docs: add obikmer user guide and MkDocs build configuration

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index_command.md

docs: add obikmer user guide and MkDocs build configuration

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merge.md

docs: add obikmer user guide and MkDocs build configuration

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pack.md

docs: add obikmer user guide and MkDocs build configuration

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phylo.md

rename distance subcommand to phylo

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predicates.md

docs: add obikmer user guide and MkDocs build configuration

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query.md

docs: add obikmer user guide and MkDocs build configuration

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reindex.md

docs: add obikmer user guide and MkDocs build configuration

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select.md

docs: add obikmer user guide and MkDocs build configuration

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superkmer.md

docs: add obikmer user guide and MkDocs build configuration

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unitig.md

docs: add obikmer user guide and MkDocs build configuration

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utils.md

docs: add obikmer user guide and MkDocs build configuration

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