If you want to use same configuration from your runtime code to find the location of your libraries, you can use the mainConfigFile option:
...if you prefer the "main" JS file configuration to be read for the build so that you do not have to duplicate the values in a separate configuration, set this property to the location of that main JS file. The first requirejs({}), require({}), requirejs.config({}), or require.config({}) call found in that file will be used.
Something like this:
({
baseUrl: "bower_components",
mainConfigFile: '/some/path/main.js', // adjust path as needed
name: "./almond/almond",
include: "./../public/main",
out: "build/main.js",
preserveLicenseComments: false
})