There is at least one v3 bug related to using non-default directories, and there could be a number of different symptoms of the same underlying problem.
A system-level method that should be returning the installation directory is instead returning the parent of the parent of the domain directory, which is fine for domain directories in the default location but not if --domaindir specifies something else entirely.
I'm not absolutely sure this is what you're seeing in your case. It has surfaced with people creating a domain using --domaindir and then deploying an app that contains an app client. I have seen some other places in the code base which uses the same API so that's why there could be other symptoms.
- Tim
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