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chore: sync master (v2.11.0) back into develop - #1309
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Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_016brRcptooQkxWr6TyWnwAE
Brings in #1271, #1272 and Benjamin's audit fixes #1274–#1288. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_016brRcptooQkxWr6TyWnwAE
Brings in Benjamin's second batch of audit fixes, #1289–#1308 (without #1301). Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_016brRcptooQkxWr6TyWnwAE
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_016brRcptooQkxWr6TyWnwAE
The -k limit is now enforced, the decoy list must match the FASTA, -a refuses input whose mates are not adjacent and counts unmapped records, quantmerge refuses ambiguous names and damaged files, and salmon_map::extend_mem takes a RefView. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_016brRcptooQkxWr6TyWnwAE
Release 2.11.0
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Brings the 2.11.0 release state back to develop:
v2.11.0).develop is an ancestor of master, so this merges without conflicts. As with 2.10.0 (#1264), use "Create a merge commit" to keep the history parallel to master.
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