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Nice work! I have felt like I lost zsh history before but never looked into it.
I have nearly a decade of zsh history. Reading that article I came to the conclusion that I may have been hit by that bug in the past but I haven’t noticed.

Then I kept reading and the author mentions accidentally exporting HISTFILE[1] and I screamed in terror and ran to my computer as I realized a mistake I’ve been making for…ever.

I am now both happy and sad I read this article.

[1] https://github.com/stapelberg/configfiles/commit/32dcda0f49a...

Does zsh have that 2000 command limit by default?

You can't expect much from a system that has those defaults, I'm all for traditions, but if I were to depend on a system for command history, it wouldn't be anything that reads a bash_history, a revolution is needed, not incremental optimizations

P.s: what I do is set it to unlimited on both size and line count, but it's not a forensic grade audit trace, we'd need an OS, or ssh command logger, preferably one that writes to an external disk, but it can be to a root controlled file, definitely not to a user owned file.

Security protects not only against attackers, but against bugs, a user's command history should not be deletable by user. Anything else is a wrong architecture that we are just carrying by inertia and laziness.

That's a bug? Happens to me with bash all the time, all I have to do is open 2 terminals at the same time... whichever one I close last is the one that writes its history. /shrug
I ran into this a few years ago (or I ran into a very similar bug). I started backing up my history file regularly because it was so annoying to lose all that history. I'll keep backing it up, but this fix is appreciated!
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this is an example of overcomplicated solutions that could be avoided with the tool we already have for years - file system - why do this "heroic" effort of "cleverly" putting everything in one file from many sessions if we could just write command history of every session into a new separate file in a directory and read all history files from the dir instead of reading one file.
A very interesting investigation, thanks for sharing
Now run AI on zsh, ask it why history would be lost and see if it can find it with no hints.
There is a whole section in the article about that
I have lost commands in the Bash history as well and I don't know why. Fortunately, I store all commands executed (+ time, return value etc.) in an sqlite database so I run a program from time to time to import that into the Bash history. The Bash history is useful for Ctrl+R
The eval bit in the end is interesting. Opus 5 and Sol 5.6 solved it reliably but Opus used 10x more tokens and room 10x as long!