`run()`: topological sort of generated files

```
> run()

[PIPELINE] Bakepipe Pipeline
   Running 2 scripts

[OK] 01_clean_data.R      (935ms)
[OK] 02_analyze_data.R    (851ms)

[SUMMARY]
   Executed 2 scripts in 1.8s
   Created/updated 3 files:
     - analysis_results.rds
     - cleaned_data.csv
     - report.txt
```