Migrate CLI parsing from clap to usage-rs

[edmundmiller]

Replace clap with usage-rs 6.1.1 for rustqc argument parsing, following the clap migration guide. QC algorithms and the BAM pass are unchanged.

What changed

• Depend on usage = { package = "usage-rs", version = "6.1.1", features = ["completions"] } instead of clap 4.
• #[derive(Parser)] / #[derive(Subcommand)] become #[derive(usage::Cli)] / #[derive(usage::Subcommands)] / #[derive(usage::Args)].
• Strandedness now derives usage::ValueEnum (still serde::Deserialize + Display). Library consumers that treated it as clap’s ValueEnum need to switch; parsing via serde YAML is unchanged.
• --version still prints crate version, git hash, build timestamp, and the runtime CPU info line. -V stays short.
• Hidden endpoints from usage: __usage_spec__ (portable KDL) and __complete_word__ (runtime completions).
• Docs/credits/AGENTS.md/CONTRIBUTING.md no longer claim clap.
• MSRV is 1.91 (usage-rs 6.1.1’s requirement; was 1.87).
• crossbeam-epoch updated to 0.9.20 for RUSTSEC-2026-0204.

cargo tree -i clap reports no clap crate in the app graph.

Intentional flag / help diffs

User-facing flags, shorts, env vars, defaults, and requiredness are the same. Parse errors and --help/--version still exit 2 / 0.

Help text is now rendered by usage, not clap’s custom help_template:

• Synopsis is rustqc rna <FLAGS> <INPUT>… rather than clap’s [OPTIONS] <INPUT>....
• Long help lists author and license from crate metadata.
• usage synthesizes a help subcommand (clap did this too by default).
• Unknown flags are rejected (unknown_flags = "error"); repeated scalar flags are rejected (args_override_self = false).
• Prefix matching is unsupported (usage does not infer --thr → --threads). Full names or declared aliases only.

Regenerating completions / docs

usage-rs is experimental; pin producers and consumers to 6.1.1.

# Dump the spec (also `Cli::to_kdl()` in-process)
cargo run --quiet -- __usage_spec__ > rustqc.usage.kdl

# Same usage-cli revision as usage-rs
usage g markdown -f rustqc.usage.kdl --out-dir docs
usage g manpage -f rustqc.usage.kdl > rustqc.1
usage g completion bash rustqc --file rustqc.usage.kdl

Shell completion scripts can also be produced in-process with Cli::completion_script(usage::complete::Shell::…).

Verification

• cargo +stable fmt --check and cargo +stable clippy -- -D warnings pass.
• cargo +stable test: 200 lib unit tests, 15 binary CLI tests, and 18 integration tests passed.
• Smoke-tested rustqc --help, -h, --version, -V, rna --help, missing --gtf (exit 2), and unknown flags (exit 2).
• First CI run failed MSRV (1.87 vs usage-rs’s 1.91) and audit (crossbeam-epoch); both are addressed in the follow-up commit.