I like my supervisor but not how he does things; What do I do?
First, research doesn't come with a specification with all details ironed out.  In most cases, many things are undefined and unknown; hence, it is called research.  We could change direction at any time, especially when we realize there is a better problem or the problem at hand is rubbish.  Consequently, the code in academia is pretty bad, poorly designed, and ad-hoc as compared to what you find in the industry; although codes in the industry can be one bowl of spaghetti too.

On your question, think about the problems at hand.  Try to plan them out as best as you can.  Collect evidence to justify the strength and weakness of a given tool/solution.   Bring these pieces of evidence to your supervisor.  If he/she is rational, he/she will either side with you or give you better reasons to not go a certain way.