Migrate CLI parsing from clap to usage-rs

.github/workflows/ci.yml

@@ -115,7 +115,7 @@ jobs:
       - name: Install Rust MSRV toolchain
         uses: dtolnay/rust-toolchain@e97e2d8cc328f1b50210efc529dca0028893a2d9 # v1
         with:
-          toolchain: "1.87"
+          toolchain: "1.91"
 
       - name: Install Linux build deps
         run: |

AGENTS.md

@@ -58,7 +58,7 @@ cargo test --test integration_test test_intercept_slope_match
 ```
 src/
   main.rs           — Entry point, dispatches subcommands
-  cli.rs            — CLI argument parsing (clap derive, subcommand structure)
+  cli.rs            — CLI argument parsing (usage-rs derive, subcommand structure)
   config.rs         — YAML configuration loading (serde), nested tool configs
   io.rs             — Shared I/O utilities (gzip-transparent file reading)
   gtf.rs            — GTF annotation file parser (with configurable attribute extraction)
@@ -243,7 +243,7 @@ To prepare a release:
 
 | Crate                  | Purpose                               |
 | ---------------------- | ------------------------------------- |
-| `clap` v4              | CLI argument parsing (derive)         |
+| `usage-rs` 6.1.1       | CLI argument parsing (derive; experimental) |
 | `rust-htslib`          | BAM file I/O (statically linked)      |
 | `plotters`             | Chart generation (PNG + SVG)          |
 | `serde`                | YAML config deserialization           |

CHANGELOG.md

@@ -1,5 +1,11 @@
 # RustQC Changelog
 
+## Unreleased
+
+### Other changes
+
+- Replace clap with [usage-rs](https://usage.jdx.dev/rust/) 6.1.1 for CLI parsing. Flags, shorts, env vars, and defaults are unchanged; help text is rendered by usage rather than clap's template. MSRV is 1.91 (usage-rs's requirement).
+
 ## [Version 0.2.1](https://github.com/seqeralabs/RustQC/releases/tag/v0.2.1) - 2026-04-09
 
 ### Bug fixes

CONTRIBUTING.md

@@ -73,14 +73,35 @@ To run all hooks manually:
 prek run --all-files
 ```
 
+## Completions, manpages, and CLI docs
+
+The CLI is declared with [usage-rs](https://usage.jdx.dev/rust/) (pinned to
+6.1.1). The binary prints its portable spec, and [usage-cli](https://usage.jdx.dev/)
+at the same version turns that spec into completions, manpages, and markdown:
+
+```bash
+# Dump the spec (also available in-process as `Cli::to_kdl()`)
+cargo run --quiet -- __usage_spec__ > rustqc.usage.kdl
+
+# Generate artifacts with usage-cli 6.1.1
+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
+```
+
+Install `usage-cli` from the same release as the `usage-rs` crate so the KDL
+round-trips. Completions are also served at runtime: with the `completions`
+feature, `rustqc` answers hidden `__complete_word__` requests from generated
+shell scripts (`Cli::completion_script`).
+
 ## Project structure
 
 RustQC is a **binary crate** with a nested module structure. All top-level modules are declared in `main.rs` (no `lib.rs`).
 
 ```
 src/
   main.rs                        Entry point, dispatches subcommands
-  cli.rs                         CLI argument parsing (clap derive)
+  cli.rs                         CLI argument parsing (usage-rs derive)
   config.rs                      YAML configuration loading (serde)
   io.rs                          Shared I/O utilities (gzip-transparent file reading)
   gtf.rs                         GTF annotation file parser