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/services/activity.ts

@@ -1,6 +1,6 @@
-import { and, desc, eq } from "drizzle-orm";
+import { and, desc, eq, isNotNull, sql } from "drizzle-orm";
 import type { Db } from "@paperclip/db";
-import { activityLog } from "@paperclip/db";
+import { activityLog, heartbeatRuns, issues } from "@paperclip/db";
 
 export interface ActivityFilters {
   companyId: string;
@@ -10,6 +10,7 @@ export interface ActivityFilters {
 }
 
 export function activityService(db: Db) {
+  const issueIdAsText = sql<string>`${issues.id}::text`;
   return {
     list: (filters: ActivityFilters) => {
       const conditions = [eq(activityLog.companyId, filters.companyId)];
@@ -27,6 +28,58 @@ export function activityService(db: Db) {
       return db.select().from(activityLog).where(and(...conditions)).orderBy(desc(activityLog.createdAt));
     },
 
+    forIssue: (issueId: string) =>
+      db
+        .select()
+        .from(activityLog)
+        .where(
+          and(
+            eq(activityLog.entityType, "issue"),
+            eq(activityLog.entityId, issueId),
+          ),
+        )
+        .orderBy(desc(activityLog.createdAt)),
+
+    runsForIssue: (issueId: string) =>
+      db
+        .selectDistinctOn([activityLog.runId], {
+          runId: activityLog.runId,
+          status: heartbeatRuns.status,
+          agentId: heartbeatRuns.agentId,
+          startedAt: heartbeatRuns.startedAt,
+          finishedAt: heartbeatRuns.finishedAt,
+          createdAt: heartbeatRuns.createdAt,
+          invocationSource: heartbeatRuns.invocationSource,
+        })
+        .from(activityLog)
+        .innerJoin(heartbeatRuns, eq(activityLog.runId, heartbeatRuns.id))
+        .where(
+          and(
+            eq(activityLog.entityType, "issue"),
+            eq(activityLog.entityId, issueId),
+            isNotNull(activityLog.runId),
+          ),
+        )
+        .orderBy(activityLog.runId, desc(heartbeatRuns.createdAt)),
+
+    issuesForRun: (runId: string) =>
+      db
+        .selectDistinctOn([issueIdAsText], {
+          issueId: issues.id,
+          title: issues.title,
+          status: issues.status,
+          priority: issues.priority,
+        })
+        .from(activityLog)
+        .innerJoin(issues, eq(activityLog.entityId, issueIdAsText))
+        .where(
+          and(
+            eq(activityLog.runId, runId),
+            eq(activityLog.entityType, "issue"),
+          ),
+        )
+        .orderBy(issueIdAsText),
+
     create: (data: typeof activityLog.$inferInsert) =>
       db
         .insert(activityLog)