Removes one level of subdirectories (and nothing apart from assets is in /run anyway) and is consistent with like every other mod's dev env

Ahh, so that's why this is a thing. They don't. Is it necessary to seperate client and server files though? The only thing that I could think of right now is to test how the mod handles configuration mismatch between client and server, since you can easily change the config files seperately. But that kinda seems like an edge case.

How do those mods handle the difference between client and server? Because in our config it is not only assets but also assets_server.

That's a good question. I have no idea if it is necessary or not to have them seperated. For me it just feels right that they are in seperate folders but I cannot put the finger on why I feel that way...

I like server and client separated as well, but I'd like /run (as with every other mod in default) and /run_server (or similar) more.

That's actually what I was going to suggest if not keeping them both in /run, except for /run-server as the server directory, since that naming style (using - as seperator) seems to be used most frequently (on Linux, at least) and you rarely see files/dirs with _ in the name. On top of that it's slightly easier to type, since you need to hold down shift to type the _