I think it might be because some of my commands reference invalid forms and maybe that breaks the list

You mean they disappear from the REPL commands dialog? Do they also disappear from the Tools | REPL | REPL commands menu?

yes from dialog, no from REPL commands in prefs

I should be able to workaround by ensuring that all commands are valid forms

but I suspect you’ll want to make it robust enough to handle invalid forms?

ah, it seems there’s some kind of duplicate command name conflict

I have project specific commands with the same name in different projects but they seem to conflict. starts working if I use different names

Ok, does this only happen when you have the projects with conflicting names open?

yes. both open at same time

global scope bug?