Harden QA reporting, thresholds, and multi-target flows

[kenahrens]

Summary

• Add PR quality comment publishing from worker runs (create/update marker-based comment) and extend operator docs for PR-report workflows.
• Add threshold-driven quality gating in app contracts/schemas and quality-report evaluation (maxBuildStderrLineDelta, maxValidationStderrLineDelta).
• Complete multi-target behavior for onboarding/intake by queueing all targets when unspecified, with CI coverage and new multi-target app/intake fixtures.
• Remove remaining active issue-first runtime paths from intake API logic and keep historical references explicitly marked as legacy context.

Validation

• npm run check
• npm run qa-integration
• npm run demo
• npm run runs -- baseline examples/apps/demo-node-multi-target/agentapp.yaml --id multi-smoke