First, this is an amazing tool so thank you for providing us that!

Now I would like to ask if is there a way to use it in a cli interface as we would like to use it in a pipeline for continuous integration. 

Ideally to maintain the integrity of the yyp and for that something like below would be really helpfull:

yyp-maker.exe /path/to/project

If it helps, here is documentation for parameter_string if it was done using game maker itself.
https://manual.gamemaker.io/beta/en/GameMaker_Language/GML_Reference/OS_And_Compiler/parameter_string.htm