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GitHub User: JamesChevalier
I handle this by keeping my edits clean, and in place of the existing options. So, rather than putting all of my customizations in one place in the file, they're spread out in the locations where the options originally appeared.
Then, I accept the changes from rails generate foundation:install for the foundation_and_overrides.scss file - allowing it to overwrite my customizations. I handle the difference(s) in git, by staging/committing all the lines that don't affect me & comparing the lines that do affect my customizations.
rails generate foundation:install
So far, I've generally been able to discard the changes to application.html.erb - I just take a quick peek at the diff from within the rails generate foundation:install command to be sure.