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Delete backup files when saving
(alien.top)
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That's what git is for, or just having undo-tree from which the file can be reverted to a previous state.
I tried to keep auto-saves and backup files in their own separate directory, since they always litter my projects which is annoying, but they just won't listen, I have to disable them.
Even for files which are being tracked in version control, I don't agree that VCS always replaces backups. In some cases, yes; but backups are to protect me from data loss, and I want that protection in more situations than VCS gives me.
I assume you mean "with a persistent undo record", which is another form of backup file, so sure -- whichever kind(s) of backup you prefer. Personally I believe I'd still want regular backups even if I used that -- if I can't trivially grep or compare old versions, I'd feel I'm missing a capability.
I keep all backups in a separate directory, and I do not experience your problem, so that sounds to me like a fixable config issue.