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This is fixed now. I ported the package to a manual module {Name} ... end system which is functionally equivalent to FromFile, but without the macro. So the docs are no longer mangled now.
I am posting this here since I am encountering the same issue myself. Here are the issues in FromFile.jl and Documenter.jl
Roger-luo/FromFile.jl#41
JuliaDocs/Documenter.jl#1781
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