For production deployment, master branch of frappe/erpnext git repository is pulled and changes are updated.
All the modifications made cannot be pushed to this master branch.
Fork erpnext repository after you login to github, All changes can be made here.
https://help.github.com/articles/fork-a-repo/
One way to keep all the updates as well as modified code is:
To modify forked repo and keep it synced with upstream and resolve conflicts.
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