refactor: extract obikindex crate and remove deprecated CLI commands

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Extracted core indexing logic, state tracking, and metadata management into a new `obikindex` crate. Refactored the `index` and `unitig` commands to leverage the `KmerIndex` abstraction and state-driven pipeline transitions. Removed obsolete CLI subcommands (`count`, `fasta`, `longtig`, `partition`) and their associated pipeline steps. Updated FASTA writing utilities for single-line output and deterministic identifiers, and refreshed workspace dependencies.

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Eric Coissac

2026-05-20 18:21:05 +02:00

parent f8cfb493b8

commit 17c9e076bd

24 changed files with 792 additions and 1593 deletions

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