Codemod db pass-through calls: messages + runs + approvals + company (C1 part 2/3)

Rewrite ~376 call sites for messages, runs, approvalsMod, and company
domains and delete the corresponding pass-through methods on
AppDatabase / AppDatabaseBase. Structural type references
(ReturnType<HandlerDeps["db"]["getRun"]>) and SweepStaleReviewsDeps-style
mocks are updated to route through the owning sub-module.

src/main/worker-service.ts

@@ -183,7 +183,7 @@ export function createWorkerService({
       const snapshot = db.listSnapshot();
       for (const run of snapshot.runs) {
         if (run.status === "running" || run.status === "queued") {
-          db.finishRun({
+          db.runs.finishRun({
             runId: run.id,
             status: "interrupted",
             summary: "Application shut down.",