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/middleware/auth.ts

@@ -13,8 +13,11 @@ export function actorMiddleware(db: Db): RequestHandler {
   return async (req, _res, next) => {
     req.actor = { type: "board", userId: "board" };
 
+    const runIdHeader = req.header("x-paperclip-run-id");
+
     const authHeader = req.header("authorization");
     if (!authHeader?.toLowerCase().startsWith("bearer ")) {
+      if (runIdHeader) req.actor.runId = runIdHeader;
       next();
       return;
     }
@@ -60,6 +63,7 @@ export function actorMiddleware(db: Db): RequestHandler {
         agentId: claims.sub,
         companyId: claims.company_id,
         keyId: undefined,
+        runId: runIdHeader || undefined,
       };
       next();
       return;
@@ -75,6 +79,7 @@ export function actorMiddleware(db: Db): RequestHandler {
       agentId: key.agentId,
       companyId: key.companyId,
       keyId: key.id,
+      runId: runIdHeader || undefined,
     };
 
     next();

server/src/middleware/logger.ts

@@ -1,5 +1,41 @@
+import path from "node:path";
+import fs from "node:fs";
 import pino from "pino";
 import { pinoHttp } from "pino-http";
 
-export const logger = pino();
-export const httpLogger = pinoHttp({ logger });
+const logDir = path.resolve(process.cwd(), ".paperclip", "logs");
+fs.mkdirSync(logDir, { recursive: true });
+
+const logFile = path.join(logDir, "server.log");
+
+const sharedOpts = {
+  translateTime: "HH:MM:ss",
+  ignore: "pid,hostname",
+};
+
+export const logger = pino({
+  level: "debug",
+}, pino.transport({
+  targets: [
+    {
+      target: "pino-pretty",
+      options: { ...sharedOpts, ignore: "pid,hostname,req,res", hideObject: true, colorize: true, destination: 1 },
+      level: "info",
+    },
+    {
+      target: "pino-pretty",
+      options: { ...sharedOpts, colorize: false, destination: logFile, mkdir: true },
+      level: "debug",
+    },
+  ],
+}));
+
+export const httpLogger = pinoHttp({
+  logger,
+  customSuccessMessage(req, res) {
+    return `${req.method} ${req.url} ${res.statusCode}`;
+  },
+  customErrorMessage(req, res) {
+    return `${req.method} ${req.url} ${res.statusCode}`;
+  },
+});