How to match patterns with nested modules

[Ahajha]

My project looks something like this:

project
    _mod1
        submod1
        submod2
        ...

_mod/submod1/submod2/... are all within one compiled extension. Note that the extension is a submodule of the main project, with the rest of it written in Python (I think this likely is fairly common, but just clarifying).

When I run stubgen, I am running from the directory above project, and I'm passing project._mod1 to stubgen, with the -r flag. This works fine, the stubs are 90% of the way there.

Now, I'm wanting to fine tune some things, and a pattern file looks like the right option. But I can't get it to match any patterns beyond really dumb things (like .*). For example, I want to try adding a prefix to a file, I've tried a number of things:

project._mod1.submod1.__prefix__:
    # hello
project._mod1.submod1.__init__.__prefix__:
    # hello
project._mod1.submod1.__init__.pyi.__prefix__:
    # hello
_mod1.submod1.__prefix__:
    # hello
_mod1.submod1.__init__.__prefix__:
    # hello
_mod1.submod1.__init__.pyi.__prefix__:
    # hello
submod1.__prefix__:
    # hello
submod1.__init__.__prefix__:
    # hello
submod1.__init__.pyi.__prefix__:
    # hello
.*submod1.*.__prefix__:
    # hello

Nothing seems to work. Any pointers would be appreciated.

I'm running on 2.4.0 with a couple backported fixes, so probably somewhere between 2.4.0 and 2.5.0.

[Ahajha]

Oh... I think it is working, but it's giving a warning regardless of if the patterns are used or not. That seems like a bug.