Refine `update-from-template` workflow

Just keeping track of some teething problems here:
- `--overwrite` is not a flag for `copier update`
- `github_repo` becomes a weird autogenerated string. Can be solved by saving it to `.copier-answers.yml` like `copyright_year`
- Files in the `template/src/{{github_repo_snake_case}}/` folder are deleted on update in the child repo. Not exactly sure why it only happens for this folder.