refactor(errors): surface 57 deferred catch-and-swallow sites via logger

The earlier sweep cleaned the hot path (worker/runtime/automation/api-
server/ipc core — 59 sites). This pass finishes the deferred long tail:
main/* services, database/* CRUD modules, api-server/* routes, ipc-*
handlers, thread-integration, automation helpers, browser, skills.

Default strategy: catch (error) { logger.warn("[module] context:", ...) }
— preserve current behavior, make the failure visible instead of
silently hidden. Widened 3 logger interface signatures to include warn
where callers only passed info/error previously (thread-helpers,
host-environment-service, ipc-domain-common).

Legitimate boundaries left intact: JSON.parse on untrusted input, DNS
resolver no-records paths, explicit safe* helpers (safeJson, parseJson,
parseTriggerDetail), URL-parse predicates, and `<unserialisable>`
fallbacks inside the prompt-builder summarisers. Each kept catch now
either has a reason in context or is a documented safe* helper.

Tests adjusted only where test-constructed no-op loggers needed a warn
stub (message-dispatch, company-mode-switch, ipc-agent-graph-handlers).

With the earlier pass, AgentCompany no longer has silently-swallowing
catch blocks in main-process or renderer business code.

src/main/desktop-shell-window.ts

@@ -12,6 +12,7 @@ import {
   session,
   shell,
 } from "electron";
+import log from "electron-log/main.js";
 import { attachWindowStatePersistence, loadWindowState } from "./window-state";
 import type { NotificationOptions } from "./notification-service";
 
@@ -96,8 +97,8 @@ export function createDesktopShellWindow(deps: DesktopShellWindowDependencies) {
     let activeRunCount = 0;
     try {
       activeRunCount = getActiveRunCount();
-    } catch {
-      // Cannot determine active runs — proceed with immediate quit as fail-safe
+    } catch (err) {
+      log.warn(`[desktop-shell-window] getActiveRunCount failed; quitting as fail-safe:`, err instanceof Error ? err.message : String(err));
       onRequestQuit();
       app.quit();
       return;
@@ -150,8 +151,8 @@ export function createDesktopShellWindow(deps: DesktopShellWindowDependencies) {
         }
       }
       // Cancel: do nothing
-    } catch {
-      // Dialog failed (e.g. window destroyed mid-flight) — quit as fail-safe
+    } catch (err) {
+      log.warn(`[desktop-shell-window] Quit confirmation dialog failed; quitting as fail-safe:`, err instanceof Error ? err.message : String(err));
       onRequestQuit();
       app.quit();
     } finally {