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You dont
We dont do it. We just have a working folder with all the source in different folders for each module. Each module has "syn", "src" and "sim" folders, with scripts for synthesis and simultion in the syn and sim folder. That way youcan synth or sim each module on it's own, with a top level folder to bring it all together.
Everything is script driven so we dont need to manage projects. The scripts will build you a project so you can investigate it when finished
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That's funny - I do the exact same thing including the same folder names. A trickier thing to handle is sharing source code between multiple projects. Most of my customers prefer to keep all projects completely separate, even if that requires a lot of file duplication. Wasteful I suppose but in some ways it does keep things simpler.
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