Add issue identifiers, activity run tracking, and migration inspection

Add issuePrefix/issueCounter to companies and issueNumber/identifier to issues
for human-readable issue IDs (e.g. PAP-42). Add runId to activity_log for
linking activity to heartbeat runs. Rework DB client to support migration
state inspection and interactive pending migration prompts at startup.
Add reopen option to issue comments validator.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

packages/db/src/migrations/0003_shallow_quentin_quire.sql

@@ -0,0 +1,5 @@
+ALTER TABLE "activity_log" ADD COLUMN "run_id" uuid;--> statement-breakpoint
+ALTER TABLE "activity_log" ADD CONSTRAINT "activity_log_run_id_heartbeat_runs_id_fk" FOREIGN KEY ("run_id") REFERENCES "public"."heartbeat_runs"("id") ON DELETE no action ON UPDATE no action;--> statement-breakpoint
+CREATE INDEX "activity_log_run_id_idx" ON "activity_log" USING btree ("run_id");--> statement-breakpoint
+CREATE INDEX "activity_log_entity_type_id_idx" ON "activity_log" USING btree ("entity_type","entity_id");--> statement-breakpoint
+ALTER TABLE "agents" DROP COLUMN "context_mode";

packages/db/src/migrations/0004_issue_identifiers.sql

@@ -0,0 +1,28 @@
+-- Add issue identifier columns to companies
+ALTER TABLE "companies" ADD COLUMN "issue_prefix" text NOT NULL DEFAULT 'PAP';--> statement-breakpoint
+ALTER TABLE "companies" ADD COLUMN "issue_counter" integer NOT NULL DEFAULT 0;--> statement-breakpoint
+
+-- Add issue identifier columns to issues
+ALTER TABLE "issues" ADD COLUMN "issue_number" integer;--> statement-breakpoint
+ALTER TABLE "issues" ADD COLUMN "identifier" text;--> statement-breakpoint
+
+-- Backfill existing issues: assign sequential issue_number per company ordered by created_at
+WITH numbered AS (
+  SELECT id, company_id, ROW_NUMBER() OVER (PARTITION BY company_id ORDER BY created_at ASC) AS rn
+  FROM issues
+)
+UPDATE issues
+SET issue_number = numbered.rn,
+    identifier = (SELECT issue_prefix FROM companies WHERE companies.id = issues.company_id) || '-' || numbered.rn
+FROM numbered
+WHERE issues.id = numbered.id;--> statement-breakpoint
+
+-- Sync each company's issue_counter to the max assigned number
+UPDATE companies
+SET issue_counter = COALESCE(
+  (SELECT MAX(issue_number) FROM issues WHERE issues.company_id = companies.id),
+  0
+);--> statement-breakpoint
+
+-- Create unique index on (company_id, identifier)
+CREATE UNIQUE INDEX "issues_company_identifier_idx" ON "issues" USING btree ("company_id","identifier");

packages/db/src/migrations/meta/_journal.json

@@ -22,6 +22,20 @@
       "when": 1771349403162,
       "tag": "0002_big_zaladane",
       "breakpoints": true
+    },
+    {
+      "idx": 3,
+      "version": "7",
+      "when": 1771456737635,
+      "tag": "0003_shallow_quentin_quire",
+      "breakpoints": true
+    },
+    {
+      "idx": 4,
+      "version": "7",
+      "when": 1771545600000,
+      "tag": "0004_issue_identifiers",
+      "breakpoints": true
     }
   ]
 }