Cleanup residual dead code and stale annotations (N-scan residual)

- Drop the "pass-through remains for back-compat" note on
  AppDatabaseBase's domain modules; the pass-through layer is gone, so
  the comment was out of date. Replace with a pointer to the ESLint
  guard that blocks regression.

- Flag the two remaining >500-line files (`agent-runtime/runtime-bridge.ts`
  648 LOC, `agent-runtime/artifact-projector.ts` 637 LOC) with an
  inline `TODO: decompose — M-followup` note. No structural change;
  the decomposition is tracked for a later milestone to keep this pass
  scope-safe.

src/main/agent-runtime/artifact-projector.ts

@@ -1,3 +1,6 @@
+// TODO: decompose — M-followup. File is 637 lines and mixes fs-walk
+// baseline capture, git-diff projection, and work-product reconciliation.
+// Split into baseline / diff / projector modules in a future milestone.
 import { isAbsolute, relative, resolve } from "node:path";
 import { execFileSync } from "node:child_process";
 import { readdirSync, statSync } from "node:fs";

src/main/agent-runtime/runtime-bridge.ts

@@ -1,3 +1,7 @@
+// TODO: decompose — M-followup. File is 648 lines; split into
+// sqlite-session-store wiring, cost/metrics routing, and hook-dispatch
+// assembly. Tracked as a future milestone; no structural change in this
+// pass.
 import type { AgentMessage } from "@mariozechner/pi-agent-core";
 import type { AppDatabase } from "@main/database";
 import type { AgentMessageRecord, DesktopEvent } from "@shared/types";

src/main/database-base.ts

@@ -52,9 +52,10 @@ export class AppDatabaseBase {
   readonly vault: SecretVault;
   protected db: DatabaseSync;
 
-  // Domain modules. New code should prefer `db.tasks.saveTask(...)` over the
-  // legacy pass-through methods on AppDatabase. Pass-through remains for
-  // back-compat until all call sites migrate.
+  // Domain modules. The canonical surface — call these directly from
+  // every consumer (`db.tasks.saveTask(...)`, not `db.saveTask(...)`).
+  // The ESLint rule in eslint.config.mjs blocks new top-level methods
+  // on AppDatabase so the old pass-through layer cannot grow back.
   public readonly threads: ReturnType<typeof buildThreadMethods>;
   public readonly company: ReturnType<typeof buildCompanyMethods>;
   public readonly agents: ReturnType<typeof buildAgentMethods>;