Server: migration prompts, structured logging, heartbeat reaping, and issue-run tracking

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>

server/src/routes/authz.ts

@@ -19,6 +19,7 @@ export function getActorInfo(req: Request) {
       actorType: "agent" as const,
       actorId: req.actor.agentId ?? "unknown-agent",
       agentId: req.actor.agentId ?? null,
+      runId: req.actor.runId ?? null,
     };
   }
 
@@ -26,5 +27,6 @@ export function getActorInfo(req: Request) {
     actorType: "user" as const,
     actorId: req.actor.userId ?? "board",
     agentId: null,
+    runId: req.actor.runId ?? null,
   };
 }