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/flows/tasks/presets/LogTask.ts

@@ -1,5 +1,6 @@
 import { Type } from "core/utils";
 import { Task } from "../Task";
+import { $console } from "core";
 
 export class LogTask extends Task<typeof LogTask.schema> {
    type = "log";
@@ -10,7 +11,7 @@ export class LogTask extends Task<typeof LogTask.schema> {
 
    async execute() {
       await new Promise((resolve) => setTimeout(resolve, this.params.delay));
-      console.log(`[DONE] LogTask: ${this.name}`);
+      $console.log(`[DONE] LogTask: ${this.name}`);
       return true;
    }
 }