cleanup: replace console.log/warn with $console, remove commented-out code

Removed various commented-out code and replaced direct `console.log` and `console.warn` usage across the codebase with `$console` from "core" for standardized logging. Also adjusted linting rules in biome.json to enable warnings for `console.log` usage.

app/src/modules/server/SystemController.ts

@@ -99,7 +99,7 @@ export class SystemController extends Controller {
          try {
             return c.json(await cb(), { status: 202 });
          } catch (e) {
-            console.error(e);
+            $console.error("config update error", e);
 
             if (e instanceof TypeInvalidError) {
                return c.json(
@@ -160,7 +160,6 @@ export class SystemController extends Controller {
          if (this.app.modules.get(module).schema().has(path)) {
             return c.json({ success: false, path, error: "Path already exists" }, { status: 400 });
          }
-         console.log("-- add", module, path, value);
 
          return await handleConfigUpdateResponse(c, async () => {
             await this.app.mutateConfig(module).patch(path, value);