fix: post-merge bug hunt — six fixes + review doc

[ypriverol]

Summary

Systematic bug review of the merged Rust port (master @ PR #31). Adds BUG_REVIEW.md documenting 11 findings; fixes the six highest-confidence issues in this PR.

Fixes (B1–B6)

ID	Area	Issue
B1	Streaming	--max-spectra bench cap dropped the final partial chunk to zero
B2	CLI routing	mzML activation auto-detect disabled when --instrument ≠ low-res
B3	TSV output	mzML runs always used MGF layout (spurious Title column)
B4	SpecE / GF	Met-cleaved N-termini used wrong terminal-mod flags in GF graph
B5	TSV output	IsotopeError column always 0
B6	CLI validation	Inverted charge/isotope ranges failed silently

Open follow-ups (documented, not in this PR)

• pepSeq dedup key ignores modifications / uses pin score not rank_score (B7–B8)
• mzML reader aborts entire file on first spectrum error (B10)
• sa_walk missed-cleavage enforcement (B9)

Test plan

• cargo test --release -p msgf-rust --test cli_smoke → 10 passed (incl. new bench-mode + charge-range tests)
• cargo test --release --workspace with 7 CI-known skips → 0 new failures

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