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I am a bit dissapointed that i have to create two separate projects one for Quartus and one for Modelsim and add same files to each projects. I create and edit files using quartus because for me Modelsim text editor is ugly and there are no features to help type code faster. Quartus atleast has autocomplete, but still im missing some features in quartus text editor to navigate through code also.
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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