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/package.json

@@ -15,12 +15,13 @@
     "@paperclip/adapter-utils": "workspace:*",
     "@paperclip/db": "workspace:*",
     "@paperclip/shared": "workspace:*",
-    "dotenv": "^17.0.1",
     "detect-port": "^2.1.0",
+    "dotenv": "^17.0.1",
     "drizzle-orm": "^0.38.4",
     "express": "^5.1.0",
     "pino": "^9.6.0",
     "pino-http": "^10.4.0",
+    "pino-pretty": "^13.1.3",
     "ws": "^8.19.0",
     "zod": "^3.24.2"
   },