The https://github.com/wikimedia-gadgets repo on GitHub is a nice place to centralize Wikimedia GitHub user scripts/gadgets/Toolforge tools. It has a lot of GitHub Members, reducing bus factor in case anyone goes inactive.
Completely up to CurbSafeCharmer, of course. Just an idea.
Can be decided after the duplicate branch/repo/bug tracker issues are fixed.
I took a look at https://en.wikipedia.org/wiki/Wikipedia:Gadget/Repositories and understood from it that this is a repo for gadgets and scripts, but reFill doesn't really fit into either category?
I think a Toolforge tool is a close enough fit. Don't think this idea that it's not a userscript or gadget needs to be a blocker.
Basically I think the wikimedia-gadgets organization on GitHub is a good place to centralize tools that don't end up in the GitHub mediawiki repo. Tools such as Twinkle, AFC helper script, shortdesc-helper, RedWarn, etc. are in the wikimedia-gadgets repo.
Up to you of course. Just my two cents. Can also ping other wikimedia-gadgets people here if you'd like reassurances.