I think there will have to be some collaboration from universities (and companies). Some not-so-refined ideas would be something like this (admittedly some problems with non-academic submissions):

- Submission requires a known affiliated email address (seems arxiv does this)

- Given a fake paper, the affiliated institute is warned and added to a known list, author(s) banned from submitting

- Second occurrence to appear on the list bans the university from submitting

"Submitting" referring to any network of conferences/journals that decide to opt into this.
This will very quickly stop authors from doing it, and universities will surely fire anyone who tries that.

For context, I am thinking of the github issue with (washington?) researchers putting bad commits/PRs

I have put software in JOSS for similar reasons you state.

Depending on how important your software is, I would consider nature methods paper. I might also try IEEE Access.

Although its been a few years so I don't remember all the details...

My only issue with JOSS is that it sometimes feels anti-academic, rather than just inclusive. Specifically, there are some issues with indexing (e.g. scopus, as I recall) that, as I read through threads about, seems the original organizers just didn't care about or think was important to the mission of JOSS.

Additionally, with the smaller page size, I think searching makes it show up less.

There are a few comments here about zenodo, but JOSS will have you use that anyway to make a doi, so i'm not sure thats really an alternative to what you are looking for.

I do support what JOSS has done and wants publishing to be. I think they have an important place. I only wish it was _also_ able to align inside of academia. From what it sounds like, you don't actually care about that though...