Instead just declare all config variables within code itself in a separate config class/module file, along with initialization to default values and provides dynamic getter/setter interface over a debug API (which can be enabled/disabled via a command line flag).
If you want, you can also provide a friendly cli tool to interact with the debug api. This tool could output help messages, show current config values - differentiate between default vs overwritten etc.
Of course, this can be written once as a utility library and cli and used consistently across all your programs.