If you want to include require.js with the main.js source, you can use this kind of command:
node ../../r.js -o baseUrl=. paths.requireLib=../../require name=main include=requireLib out=main-built.js
Since "require" is a reserved dependency name, you create a "requireLib" dependency and map it to the require.js file.
Once that optimization is done, you can change the script tag to reference "main-built.js" instead of "require.js", and your optimized project will only need to make one script request.