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/user.ts

@@ -169,6 +169,7 @@ async function token(app: App, options: any) {
    }
    $log.info(`User found: ${c.cyan(user.email)}`);
 
+   // biome-ignore lint/suspicious/noConsoleLog:
    console.log(
       `\n${c.dim("Token:")}\n${c.yellow(await app.module.auth.authenticator.jwt(user))}\n`,
    );