We have faced these few issues within ERPNext:-
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Migration and Rollback process is not well defined and design in ERPNext, which creates a big issues with Production Server.
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Any change in previous Design and major Functionality change should validate existing Data on server which is also missing, results in Breakages of Production server.
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Regular updates and changes required in Documentation part as well.
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These all major changes results in data validation and data loss which is not acceptable in production servers.
I believe these are major pin points for every user of ERPNext, so decided to share with you. Hopefully you will consider it quickly.