Equivalent to basePath in CLI?

When I generate code with cli-build-app I get the code in output that I expect, but when I go to replace the html code that I had in my java server paths it does not work because it cannot find the files referenced (eg. main.js, etc) because its current directory is different. Is there documentation that talks about how to fit Dojo 2.0 output into existing projects?

I eject and modify base.config.js in “config/build-app/”