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I assume that the changes have been made directly to the JSON/py/js file?
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When you change anything in the core code, it creates an update problem as there is a difference in the commit history made locally v/s in the incoming changes. Check
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If you want to keep these changes, stash them and re-apply the changes.
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If you do not want to keep the changes, you can go to the frappe directory and reset it:
git reset --hard
. Or pass the reset flag when updating bench:bench update --reset
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When making changes, it is best to avoid code changes directly until unavoidable. For adding fields you can look at custom field option. For making server-side changes, you have the option of custom apps and server scripts, same for js changes.