remove_files.py

#!/usr/bin/python3
import yaml
import sys
import os
import os.path


def valid(element_name):
    return os.path.exists(f"elements/{element_name}")


def main(filename):
   with open(filename) as file:
       data = yaml.load(file, Loader=yaml.CLoader)

   for project, elements in data["projects"].items():
       data["projects"][project] = {key: value for key, value in elements.items() if valid(key)}

   with open(filename, "w") as file:
       yaml.dump(data, file, Dumper=yaml.CDumper)

if __name__ == "__main__":
    main(sys.argv[1])