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Benchmarking - #2
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Allow recurrent and multiallelic mutations in MatcherIndexes. The C library takes optional per-site ancestral states and per-mutation derived states, and validates them against num_alleles; without them the behaviour is unchanged (ancestral 0, derived 1). The Python MatcherIndexes wrapper encodes states from the tree sequence via the new alleles argument.
Scripts to prepare the sc2ts ARG for both engines, generate copy and synthetic recombinant queries with known ground truth, and run the tsinfer and tskit Viterbi engines over them, recording timings, paths and comparable path likelihoods.
Make nested sub-ARGs of the benchmark ARG, each the ARG as of an earlier date: all nodes at least as old as a time cutoff, with ancestry no longer above any sample pruned. All sites are kept so a query set can run against every sub-ARG, and node IDs are reported as full-ARG IDs so results compare across sizes. The README records the findings from the first scaling runs, including tskit-hmm's suboptimal results with internal samples.
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