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/cli/commands/copy-assets.ts

@@ -32,5 +32,6 @@ async function action(options: { out?: string; clean?: boolean }) {
    // delete ".vite" directory in out
    await fs.rm(path.resolve(out, ".vite"), { recursive: true });
 
+   // biome-ignore lint/suspicious/noConsoleLog:
    console.log(c.green(`Assets copied to: ${c.bold(out)}`));
 }