How to deal with scooping when doing open-source tools development?
Having developed academic open source software for 20 years, I have never heard anyone getting "scooped" by putting code out there. And I know lots of people who do all of their development out in the open, often years before they have it all together to make it into a publication.

I believe that the reason why this never happens is that it's difficult to take someone else's code and understand it in sufficient detail without the author's deep familiarity with the subject. Certainly to understand it at a level that would allow that person to write up a publication about it and claim that it's their own invention. (That's in addition to the fact that everyone knows that that would be unethical.) It's so much easier to collaborate with the original author if one had to add something because then one would have the person who understands it all help you with it.

So I wouldn't worry about this. Put stuff out there and see that people use it. You'll build a reputation that way, and that's what you're going for. If you keep things secret, nobody will know it but you also aren't going to gain any reputation points for it.