What is the best practice for working with a project as nested modules?
I use the version with double indent and I think it is the common usage:

module ProjectName
    module SubModule
        # Double indent for all the code in the file!?
    end
end


If you don't like the double indention, just don't do it. 

It is best practice to indent each code level (module, class, def, loops...), but no must.
In Python it is part of the syntax, but not in Ruby.

See also https://stackoverflow.com/questions/3833641/is-there-an-acceptable-way-of-putting-multiple-module-declarations-on-the-same-l