fix setting boolean command line arguments in config file #225
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The default value when using `store_true` is `False`. As a result this will always overwrite any value set in the config file. This fixes this and will only overwrite a potential value in the config file when using the flag.
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The default value when using
store_trueparameters isFalse. As a result this will always overwrite any value set in the config file. This fixes this by changing the default toNone, so a potential value in the config file is only overwritten when using the flag.