Before deploying, Plug in Git checks for any changes to the current theme in Shopify.
If changes are found, Plug in Git will import them to GitHub and merge them into the master branch.
If there are no conflicts, Plug in Git will deploy the master branch to Shopify. The theme that is on master branch will completely replace the current theme on Shopify and become the new current theme.
The replaced current theme of Shopify will be saved as theme copy in the Shopify admin.
If there are merge conflicts Plug in Git will delay the automatic deploy until the merge conflicts have been manually resolved.