Eliminate flag duplication when using CodeChecker config file

[bruntib]

When #3655 lands, CLI arguments will be present twice in analyzer_config after all arguments are parsed. This is because the CLI arguments are parsed to check the value of --config, that file is parsed and prepended to the CLI argument list, and that whole thing is parsed again.

This isn't an immediate concern (the latest argument will come to effect, which will be the CLI one), but isn't too pretty either. We should likely not parse all command line arguments twice anyways.