Unify MetaUmbra manifest annotation workflow

[byemaxx]

What changed

• Add a strict loader for metaumbra.genome_selection_manifest.v1 and one manifest-driven OTF backend for single- and multi-unit annotation.
• Keep explicit non-MetaUmbra sources: MetaX automatic genome selection and custom genome lists.
• Preserve custom intensity prefixes and correct automatic/custom-list provenance.
• Keep analysis_unit_id in canonical manifest OTF output, including __global__.
• Reorganize the Peptide Annotator GUI around source, inputs, validation, output, and advanced settings.
• Validate empty threshold genome lists and make Windows console progress output encoding-safe.
• Update CLI/result JSON, workflow recorder, documentation, cross-repository contract tests, and GUI/backend tests.

Why

The earlier implementation inferred modes across separate global and unit-specific paths. That duplicated scientific behavior, produced inconsistent downstream schemas, and caused regressions in non-manifest annotation settings.

Impact

MetaUmbra-driven annotation now consumes the unified manifest contract. Existing MetaX automatic and custom-list annotation remain supported through explicit source selection.

Validation

• Annotation/analyzer/workflow regression selection: 75 passed
• Final manifest, CLI, backend, GUI-layout, console, and cross-repository focused suite: 23 passed
• Real global OTF: 29,437 rows with analysis_unit_id=__global__
• Real three-unit OTF: 84,390 rows, no duplicate (analysis_unit_id, Sequence)
• Real automatic and custom-list runs validated with an Abundance intensity prefix
• git diff --check passed

[byemaxx]

@codex

[chatgpt-codex-connector]

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[byemaxx]

Ready to merge.

The review feedback and follow-up hardening are complete:

• initialized QApplication before constructing GUI widgets;
• made manifest loading strictly validate required fields, list types, uniqueness, and threshold relationships;
• added fail-fast checks for missing or duplicate selected genome TSV files without rereading TSV contents;
• added the pinned MetaUmbra producer contract test to CI.

Validation at head 256af84:

• focused/regression suite: 102 passed;
• GitHub Actions: 6/6 passed;
• all review threads resolved;
• merge state: CLEAN.

The added runtime work is limited to linear validation of manifest metadata and already-enumerated file names, so no meaningful annotation-performance regression is expected.