Copilot

Add comprehensive change logging for policy object modifications including complex objects, policy rules, role assignments, and all assignment fields

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## Enhancement: Comprehensive Change Logging for Policy Objects Implemented detailed change logging for all policy object modifications to the Output folder, providing complete visibility into what changed for change management...

This PR adds [loom](https://github.com/tokio-rs/loom) testing to detect concurrency bugs like deadlocks and data races in the Rust codebase. The implementation uses a conditional sync primitives approach to enable loom testing...

Store PeptideIndexer settings as metavalues in SearchParameters

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## Description PeptideIndexer now stores its runtime settings as metavalues in SearchParameters (following the pattern used by other tools like PercolatorAdapter). This provides traceability for analysis parameters, particularly the automatically...

Fix CometAdapter configure-time check and enable DatabaseSuitability tests

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## Description `OPENMS_FINDBINARY` was used to find CometAdapter at configure time, but CometAdapter is a built TOPP tool that only exists after compilation. This caused the check to always fail,...

Use external libraries from Debian repos to prevent deb package conflicts

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## Description OpenMS deb packages conflicted with system sqlite3 installations due to bundled libraries. When USE_EXTERNAL_SQLITECPP is enabled, the build uses system libraries instead of vendored versions, preventing file collisions....

Generate ApplicationsComponent.plist for macOS PKG installer bundles

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## Description Implements automatic generation of `ApplicationsComponent.plist` during CMake configure step for macOS PKG packages. The plist lists all GUI application bundles (TOPPView, TOPPAS, INIFileEditor, SwathWizard, FLASHDeconvWizard) with `RootRelativeBundlePath` and...

wip: feat(USI): Add Universal Spectrum Identifier utility class with PeptideIdentification integration

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- [x] Design USI class structure and helper methods - [x] Create USI utility class header and implementation - [x] Add unit tests for USI functionality - [x] Add USI...

Add ProteomicsLFQ TOPP test for IBAQ quantification method

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## Description Adds test coverage for IBAQ (Intensity-Based Absolute Quantification) protein quantification in ProteomicsLFQ. IBAQ normalizes protein abundances by dividing summed peptide intensities by the number of theoretically observable tryptic...

Fix macOS PKG installer bundle relocation issues for TOPPAS

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## Description The macOS PKG installer was relocating TOPPAS.app to incorrect locations instead of installing to the target directory. Two relocation scenarios were identified: 1. **Relocation to old installation**: TOPPAS.app...

Add molecular multiplier support for multimer adduct annotation

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MetaboliteAdductDecharger cannot annotate multimeric adducts like [2M+H]+. While the adduct TSV files already contain these entries (e.g., `2M+H;1+`), the `Adduct` class used by `MetaboliteFeatureDeconvolution` has no concept of molecular multipliers....