Javaplex (https://github.com/appliedtopology/javaplex ) is a software package for use in computing persistent homology in topological data analysis. Would questions for use with software like this belong on stackexchange proper (since it's about a computer program), or on math.stackexchange, since the whole program is for computing things in math, or somewhere else?
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Questions related to mathematical software and programming can be on-topic on this site if they are to a relevant part mathematical questions. The mere fact that the questions arises in relation to solving mathematical problems does not make the question itself mathematical.
I assume by "stackexchange proper" you mean Stack Overflow. That site is for question on programming; if your question is a question on programming it may be on-topic there. In the past a few questions on it were posted there and two out of three I could find received an answer there.
Other SE sites you could consider are Computational Science, possibly the best choice, and maybe the statistics site Cross Validated.
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$\begingroup$ Check, will give computational science a try. The math part is simple, I just want to change the metric it uses from euclidean to a custom metric, so it really is just about the code $\endgroup$– AlanCommented May 13, 2017 at 22:47