Error logs

[mzueva]

Write refusals to stderr as well as stdout, so the platform's error dialog shows them

Greptile Summary

The PR writes user-facing analysis refusals to both stdout and stderr so they remain in the run log and also appear in the platform error dialog. No actionable defects were identified.

• Adds stderr emission while preserving stdout emission and the non-zero exit status.
• Extends CLI integration tests to require refusal details on both streams.
• Adds a patch changeset explaining the platform runner behavior and updates the organization logo.
• Important touched terms: Refusal — a user-correctable data-validation failure that stops analysis without producing partial output; its diagnostic is now duplicated to stderr. stdout — the command’s standard output stream retained as the run audit log; its refusal behavior is unchanged. stderr — the command’s standard error stream used by the platform’s failed-command dialog; it now receives refusal diagnostics. Latest output — the platform error-dialog text populated from stderr; it now includes the concrete refusal reason.

Confidence Score: 5/5

The PR appears safe to merge, with refusal details deliberately routed to the two distinct platform-facing output channels.

The refusal branch retains its existing stdout diagnostic and exit behavior, adds a valid stderr write, and the updated integration tests cover the reachable validation failures.

Important Files Changed

Filename	Overview
software/src/main.py	Duplicates refusal diagnostics to stderr while preserving stdout output, no-partial-output behavior, and exit status 1.
software/tests/integration/test_cli.py	Updates three reachable refusal scenarios to assert that their diagnostic text appears on both output streams.
.changeset/refusals-to-stderr.md	Adds an accurate patch release note explaining why refusal messages must reach stderr.
block/logos/organization-logo.png	Replaces the organization logo asset without affecting analysis execution.

Flowchart

%%{init: {'theme': 'neutral'}}%%
flowchart LR
  V[Validation failure] --> R[Refusal handler]
  R --> O[stdout: run log]
  R --> E[stderr: platform error dialog]
  R --> X[Exit status 1]

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Context used (4)

• Context used - Terms is a types in codebase. Provide the list of ... (source)
• Knowledge Base — Sequence input validation
• Knowledge Base — Sequence analysis execution
• Knowledge Base — Analysis test coverage