Investigate on the possibility to remove the generated files.

[huxuan]

• Remove generated files and leverage skip_if_exists for necessary files.
• Remove consistency check in Makefile
• Remove consistency check in GitHub Actions
• Remove consistency check in GitLab CI/CD

File list to be kept when regenerate the project (make consistency):

• .git
• template\
• includes\
• copier.yaml
• pdm.lock

Extra file list to be kept (TBD):

• .github\
• .gitlab\
• .gitlab-ci.yml
• Makefile

[huxuan]

This does not seem to be a blocking issue for release the beta version.