You reference the GitHub repo of your public (or with a little extra work, private) fork of Solidus from your Gemfile to run your app against it.

yah, but what if i need to modify the source code of spree? where to modify?

I'm not sure what you're asking exactly. Most customizations for your store are made using decorators, deface overrides, and overriding views in your codebase, not in Solidus. If you're making changes to Solidus to PR upstream, you'd commit your changes to Solidus and push them to your public fork on GitHub.