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Synced 4 upstream commits (lazear#220 deisotope charges, lazear#228 Bruker file://, LDA/LR streaming perf, lazear#225 SoA representation). Conflict resolution: the fork's AoS ProcessedSpectrum<Peak> + peak_charges deliberately diverges from upstream lazear#225's SoA (masses/intensities/charges parallel arrays). Kept the fork's version verbatim for representation-coupled files (rejecting lazear#225 there); the fork already provides lazear#220's charge-tracking and lazear#228's file:// handling. All other upstream improvements (ml LDA/LR streaming perf, database/ion_series/peptide/fdr/enzyme) taken via clean merge. Files kept at fork version: sage/src/{spectrum,scoring,tmt,lfq}.rs, sage-cli/src/{runner,output}.rs, sage-cli/tests/integration.rs, sage-cloudpath/src/util.rs. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Rebase #178 and complete implementation