Modify themes or php, and updates will overwrite them the next time a theme or WB update becomes available. This seems to be a fundamental problem.
What strategies or tool sets can you recommend to deal with this - it sounds like a workflow question to me - I have looked for an explanation, tutorial, or general discussion around this issue - surprisingly, they do not seem to be out there.
Maybe they are, but if so, I do not know what people call this issue.
Anyway, I am hoping someone will be able to send me to a workflow tutorial that deals specifically with this problem.
I know I can keep backups before updating, but if I modify a php file, and the development team at WP changed that same file, then putting my older file in to replace the newer one would certainly be counter productive, and could break the system.
Anyone have any thought on this?