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Hi Bernard,
You can push your changes to the erpnext repository into your fork,
change the production git repo to point to your fork and then bench
update should work for you. In this case, you'll have to manage
pulling from upstream yourself.
A more maintainable way would be to try to achieve this via another
app that would not require you to fork erpnext.
My suggestion is to make the new doctype in a new custom app and make
a link field/ table in HR/Employee via "customize form" feature.
Thanks,
--
Pratik
erpnext