Integrate the Configuration module in other modules

[sinaahmadi]

The Configuration module needs to be properly integrated into each single function in all other modules. This is not the case for Stem module, for instance. https://github.com/sinaahmadi/klpt/blob/d540c52a7cf86e249ab0c9cc9f6d7b524e31d6a9/klpt/configuration.py#L18