[labkey-jeckels]

Rationale

This PR fixes a batch of TargetedMS exceptions reported to mothership across chromatogram rendering, Skyline import, QC outlier calculation, and the QC plot/summary pages. Two of the fixes also correct wrong behavior rather than just suppressing the error: the replicate annotation filter on the peptide/molecule chromatogram grid never worked, and small-molecule precursor chromatograms could map transitions to the wrong traces when a transition filter was active.

Triage notes for these mothership reports: https://claude.ai/artifact/CtxKZANKRqfhZxs7PHEqBr

Changes

• Chromatogram charts tolerate duplicate series labels, missing sample files or replicates, and transition/chromatogram count mismatches instead of throwing
• Replicate annotation filtering on the precursor chromatogram grid now produces valid LabKey SQL
• Small-molecule precursor chromatograms align each transition with its own chromatogram trace, matching the peptide behavior
• Skyline import fails cleanly when the run is deleted mid-import, and QC outlier calculation handles folders with no metrics
• QC plot, QC summary, and peptide heatmap pages guard against missing metrics, data rows, and DOM elements, and stale tooltips
• Added a unit test for duplicate series labels and a Selenium test for the replicate annotation filter

Tasks

• Claude Code Review
• Manual Testing - not needed
• Test Automation