fix: harden parser and pipeline output handling

[LessUp]

Summary

• harden FASTQ parsing so blank separator lines fail instead of truncating input
• preserve pipeline outcome metadata and honor save_reorder_map consistently
• remove non-UTF-8 output-path panics by using Path-based writer APIs and add regression coverage

Test Plan

• cargo fmt --all -- --check
• cargo clippy --all-targets -- -D warnings
• cargo test --lib --tests
• cargo doc --no-deps
• npm run docs:build