refactor: implement RoutableSuperKmer and update k-mer indexing pipeline
Replace raw SuperkMer routing with a new RoutableSuperKimer type that embeds canonical sequences and precomputed minimizers, enabling direct partition routing via hash. Update the build pipeline to yield RoutableSuperKmers throughout (builder, scatterer), refactor FASTA/unitig export commands to use the new type and compressed outputs (.fasta.gz, .unitigs.fasta.zst), revise SuperKmer header to store n_kmers instead of seql (avoiding 256-byte wrap), and update documentation to reflect minimizer-based theory, two evidence-encoding strategies for unitig-MPHF indexing (global offset vs. ID+rank), and the new obipipeline library architecture with parallel workers, biased scheduling, and error handling.
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@@ -1590,6 +1590,9 @@ name = "obikmer"
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version = "0.1.0"
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dependencies = [
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"clap",
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"memmap2",
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"niffler 3.0.0",
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"obidebruinj",
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"obifastwrite",
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"obikpartitionner",
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"obikrope",
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@@ -1597,7 +1600,10 @@ dependencies = [
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"obipipeline",
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"obiread",
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"obiskbuilder",
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"obiskio",
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"ph",
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"pprof",
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"rayon",
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"tracing",
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"tracing-subscriber",
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]
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@@ -1633,6 +1639,8 @@ version = "0.1.0"
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dependencies = [
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"bitvec",
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"criterion2",
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"serde",
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"serde_json",
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"xxhash-rust",
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]
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