/
..Common/Scripts/Script1.js
..Sharepoint2010/Layout/Scripts/[reference to Script1.js]
..Sharepoint2013/Layout/Scripts/[reference to Script1.js]
Developement for Sharepoint allows to deploy resources such as js and css files. Different versions of Sharepoint have different metadata (project types, webparts, paths), but the source js/css are the same.
Programmatically it's best to have a signle copy of resource and use it from these different projects.
So editing Script1 in Sharepoint2010 project and saving it eventually result in updated Common/Script1.js which will be i.e. updated automatically for Sharepoint2013.
I'm relatively new to sharepoint, but I'm not searching for "use build options, cmd xcopy /sp2010/script1.js common/scripts/script1.js".
I'm using WebEssentials to simplify development, there are bundles, which defines path to resources and then compile these resources, but that doesn't work with the given scheme.
If I understood your problem correctly, "Add as link" option in Visual Studio can help you. The article is actually about Win8 development, but whatever.