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rubik
-i (index server) & -y (force "yes") options should be global
We have some refactor to do about it, I tried something quick from my side but it ended being more complex than expected. In the same way, I also suggest to drop the "/pypi" suffix in the server address and just assume /pypi & /packages is available. It will help us a lot while testing (we can use a custom pypi server or proxy for instance) .
About the "yes" option, I suggest it's something global and not "per action", I mean, instead of setting ['update']['yes'] ['install']['yes'] etc... it should always ask if not forced otherwise from the code, or never ask if the user set --yes. That sounds easy but that means providing constructor parameters instead of objects reading directly the content of the current configuration... do you agree with my analyse ?
Btw, this is a minor issue now which is just a brake while testing... I'll write more tests now for the features to be released...