fix: stabilize annotation CLI integration

[byemaxx]

Summary

• pass multiple MetaUmbra digest directories through its actual single-value delimiter contract
• make global genome-selection inference and validation consistent across CLI and GUI
• resolve configuration-file paths relative to the configuration file while preserving CLI override semantics
• preserve existing scientific outputs by selecting a collision-free actual output path, while atomically replacing the requested result JSON
• terminate subprocess trees on cancellation and retain the CLI exit-130/result contract
• expand installation-profile CI coverage, including Windows annotation integration tests

Root cause

The integration layer previously treated MetaUmbra digest directories like repeated argv values even though MetaUmbra accepts one delimited value. Selection inference, metadata, config-relative paths, output collisions, and subprocess cancellation were also handled in separate places, which allowed contradictory or incomplete behavior.

Compatibility and impact

• No peptide mapping, LCA, intensity, aggregation, or other scientific calculation method was changed.
• The annotation result schema remains 2.0 and the workflow API remains 1.0.
• This intentionally cleans up contradictory selection configurations rather than preserving them.
• No IterDIA-specific code or README documentation is added.

Validation

• 117 passed, 2 warnings in the focused annotation/integration suite
• 324 passed, 31 warnings in the complete local test suite
• real MetaUmbra parser verified with multiple digest directories containing spaces
• lightweight/base import verified without PyQt
• GitHub Actions workflow YAML parsed successfully
• git diff --check passed

[byemaxx]

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[chatgpt-codex-connector]

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[chatgpt-codex-connector]

Avoid returning before killing the process group

When cancellation happens after the process-group leader has exited but its descendants are still alive (for example a helper that spawned digested-scan workers which keep stdout open), this early return skips os.killpg(...) even though run_streaming_subprocess starts the command in a new session. In that state the CLI can report cancellation while orphaned worker processes continue running; for process_group=True, attempt to terminate the group even if poll() says the direct child is already gone.

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