Replace auto-migrate-if-empty with interactive migration flow that inspects
pending migrations and prompts before applying. Add pino-pretty for structured
console + file logging. Add reapOrphanedRuns to clean up stuck heartbeat runs
on startup and periodically. Track runId through auth middleware, activity logs,
and all mutation routes. Add issue-run cross-reference queries, live-run and
active-run endpoints for issues, issue identifier lookup, reopen-via-comment
flow, and done/cancelled -> todo status transitions.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
a90063415e