Fix config loading without source name

[Mirochill]

Summary

• ignore unset CLI options when loading a config file so values like project_name from the file are preserved
• merge config file values with provided CLI values explicitly, with provided CLI values taking precedence
• report a clear Typer validation error when neither a source name nor project_name is available

Fixes #126
Fixes #137

Validation

• git diff --check
• inspected the changed config loading and CLI project directory guard
• Not run locally