Release simpleaf 0.28 integration

[rob-p]

Summary

• add shared typed barcode-correction and resource option groups for standard RNA, multiplex RNA, and ATAC
• forward only explicit overrides so alevin-fry remains the source of protocol defaults
• keep the legacy sample-correction alias hidden and translate it to the new spellings
• require alevin-fry 0.18.0 and apply a warning-based two-thread floor consistently across every child stage
• add validation, CLI snapshots, strict rustdoc CI, and live Astro documentation
• retire the obsolete release script in favor of bump_and_publish.sh
• keep ATAC peak calling genuinely opt-in instead of requiring MACS after a successful non-peak pipeline

Validation

• 71 unit tests, CLI snapshots, four CLI smoke tests, and one regression test pass
• formatting, strict clippy, strict rustdoc, and git diff checks pass
• clean build passes with the CMake module loaded
• Astro production documentation build passes under Node 20
• ordinary RNA GPL/collate/quant passed against crates.io-installed alevin-fry 0.18.0
• multiplex/Flex mapping/GPL/collate/quant passed against that published executable while exercising every new cell, sample, memory, temp-directory, and orientation forwarding route
• ATAC mapping/GPL/sort passed against that published executable with Frequency correction and without MACS installed or requested
• all three smoke pipelines requested one thread, emitted the practical-minimum warning, and consistently passed two threads to every child stage

Final release step

After merge, delete the completed temporary integration checklist, run the sole documented release script to bump and publish 0.28.0, and tag the exact published commit.