The database had a lot of free pages due to a large number of row deletes over time. The Laravel Pulse package was the main cause of these deletes (recording entries and then deleting them after a period), but cache, jobs, etc also contributed to the free space that could be truncated off the file.
Interesting indeed, do you mean that you've been working with laravel pulse using sqlite database?
Yes. Pinkary is currently using Laravel Pulse, saving entries to the production database (which is sqlite).