Build spectral libraries from charged peptide TSV

[jspaezp]

Summary

Add timsseek build-library --peptides peptides.tsv for charged ProForma and protein IDs. Predict each specified modification and charge, preserve supplied decoys, and generate pseudo-reversed or seeded shuffled decoys. Generated decoys cannot match a target at any charge. Pseudo-reverse retries with shorter interior spans; if every candidate collides, the target remains unpaired.

Use one numeric msspeculator:decoy_group for FASTA and peptide libraries. Supplied TSV group IDs must be integers; the builder assigns unique IDs to targets without one. The mzSpecLib reader and in-memory prediction path retain numeric IDs. The old decoy_pair_id term is removed.

TalusBio/msspeculator#18 and #19 are merged. Pinned to #19's merge commit, 3fb9dddbd848f4e7ccf3ccfc049690d2f10431a9.

Checks

• task fmt
• cargo test -p timsseek_cli --test build_library --no-default-features --offline (5 passed)
• cargo test -p timsquery --lib serde::mzspeclib_io --offline (34 passed)
• cargo test -p timsseek_cli --bin timsseek --no-default-features --offline (110 passed)
• cargo clippy -p timsseek_cli -p timsquery --no-default-features --all-targets --offline -- -D warnings -A clippy::redundant_closure

Strict Clippy has an existing redundant_closure warning in rust/timsseek/src/utils/maybe_par.rs:54.