Replace `dotenv` by `--env-file`

[ericcornelissen]

Relates to #1976 (comment)

Summary

This issue exists to remove the dependency on the package dotenv in place of the --env-file option from Node.js (and update the eslint-plugin-depend config accordingly).

This is currently blocked by the --env-file option not being available when invoking an npx command (which we need when fuzzing).