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When saving changes to a theme to which it does not have write permissions, the file_put_contents function will output an error in debug.log.
But the plugin will still say it succeeded in the editor. This leads to the destruction of user changes, without them being saved to the files
The error:
[24-Apr-2025 17:46:58 UTC] PHP Warning: file_put_contents(/var/www/html/wp-content/themes/qip-wp-themes/merryclaude2025/theme.json): Failed to open stream: Permission denied in /var/www/html/wp-content/plugins/create-block-theme/includes/create-theme/theme-json.php on line 6
After fixing the permissions, the plugin saved perfectly.