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/AppFlows.ts

@@ -25,7 +25,6 @@ export class AppFlows extends Module<typeof flowsConfigSchema> {
    }
 
    override async build() {
-      //console.log("building flows", this.config);
       const flows = transformObject(this.config.flows, (flowConfig, name) => {
          return Flow.fromObject(name, flowConfig as any, TASKS);
       });