[bot] Merge 25.11 to 26.3 (Conflicts)#1214
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…on (#1211) * Extract TargetedMSHelper and add upgrade test for 26.3 schema migration Extracts setupFolder(), selectFolderType(), and importData() from TargetedMSTest into a new TargetedMSHelper class so the logic can be shared without subclassing. Adds TargetedMSUpgradeTest to verify the targetedms-26.006-26.007 migration correctly populates PeptideGroupCount, MoleculeGroupCount, and ProteinCount on existing runs. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * Split upgrade test into pre- and post-upgrade count checks testPreUpgradeCounts queries columns available in 25.11 (Peptides, SmallMolecules, Replicates) and runs on both setup and verify phases. testPostUpgradeCounts is gated with @EarliestVersion("26.3") and Assume.assumeFalse(isUpgradeSetupPhase) so it only runs on the new server after the 26.006-26.007 migration. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * Fix field names * Not ready for Java 25 yet * Fix annotations --------- Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>
…flicts from 25.11
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