Follow-up: reorganize main.rs command dispatch and split cli.rs

[cjfields]

Follow-up to the module reorg in #66 (LOESS → loess.rs, WFA → wfa.rs, lib crate introduced). That pass deliberately left the two largest files untouched to keep the diff reviewable. This issue tracks the remaining structural cleanup.

main.rs (~4.6k lines)

It's a god-file: CLI dispatch plus the full inline orchestration for all ~21 Commands::X subcommands plus ~20 helpers. With the dada2_rs lib crate now in place (#66), command handlers can move out cleanly.

Options considered previously:

• Grouped handlers (recommended starting point): group related commands into a few modules — e.g. commands/dada.rs (dada / dada-pooled / dada-pseudo), commands/chimera.rs, commands/taxonomy.rs (assign-taxonomy / assign-species / tax-to-tsv), commands/seqtable.rs (make-sequence-table / seqtable-to-tsv|fasta), commands/errors.rs (learn-errors / errors-from-sample / kdist-calibrate). main.rs shrinks to argument parsing + dispatch.
• Full per-command modules (src/commands/<name>.rs per arm) — cleanest end state, most churn.

Constraint: keep each handler's logic behavior-preserving; verify with the existing concordance/parity tests + byte-identical outputs.

cli.rs (~2.2k lines)

Structurally fine (clap Commands enum + arg structs) but large. Lower priority — consider splitting the clap definitions per command group only if it aids navigation, or leave as-is.

Acceptance

• No behavior change (byte-identical outputs; full test suite green on default and --features wfa).
• main.rs reduced to dispatch + shared helpers.
• No performance regression (hot code already lives in the lib crate).