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Sorry for a late reply, I didn't have an answer right away so it ended up on a back burner.
What do you mean by having functions in Main? Do you mean extending functions in e.g. Base or other packages? When building package docs the Main should basically be the make.jl file, and if you're documenting a package then you shouldn't have any functions there.
To get your docstrings for functions extending functions from e.g. Base, you should be able to do Base.foo. And this should exclude the docstrings from Base and only take docstrings from MyModule.
In any case, an example where the issue comes up might be best.
I have a bunch of functions in MyModule, another bunch in Main that I would like to use @docs with.
The last one surprised me, I thought modules=[...] was only for generating warnings, why does it effect whether docstrings are found?
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