File lock issue
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For some time, when I open kitty terminal on macOS, I always see the following warning message:

zsh: locking failed for /Users/jdhao/.histfile: operation not permitted: reading anyway

This may be because the HOME directory is locked (for me, this is the case). To unlock the directory, open the Finder and click the $HOME directory, press Command + i to get the file info. Under the General section, make sure that the Locked button is unchecked.

To change the file lock state on the command line, use chflag:

chflag -R nouchg /path/to/directory

After restarting the terminal emulator, the issue should be gone.

Operation permission issue
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Another issue I often get is that when I use ls or rm on some files, I often get a message like the following:

ls ~/Library/Messages ls: Messages: Operation not permitted

This is due to the disk access issue. Open macOS Security & Privacy settings and go to Privacy tab. Give your terminal emulator Full Disk Access.

Restart your terminal and the issue will be fixed.