It doesn’t matter how it happened, it doesn’t matter why, blame can (and probably will) be placed later. What matters now is that your production MySQL database was just deleted from the filesystem while the MySQL daemon was running. The good news is that the server, somehow, is still running fine, and the system is still up. The bad news is that the directory where MySQL stores the database is now empty.

Take a deep breath, you are running Linux, here is what to do:

Default operating system installs on a server are almost always wrong. Unfortunate, but true. In an attempt to build a generic system that appeals to as many situations as possible, the default install is often overloaded with software that is not necessary, and a filesystem layout that would allow one rogue daemon to fill up the entire drive. This is wrong, but easily remedied. A little extra care during the installation and initial setup of the server will result in a system that is smaller, cleaner, easier to maintain, and more secure than what ships on a default install.

FreeBSD has a long and strange history, tracing its roots back to the original Unix from Bell Labs. FreeBSD can almost be seen as the older brother to the younger, more popular Linux. While they are similar, FreeBSD’s long history has given it a very different philosophy and purpose. You can, and many people do, run FreeBSD as a desktop OS, but that’s not where the systems real talent lies. While Linux has tried, and in many cases succeeded, to be everywhere that a kernel can run, FreeBSD has decided that it belongs in the datacenter, a belief that is personified in the FreeBSD slogan, “The Power to Serve”. FreeBSD’s Jails are a great example of where the philosophy of Linux and FreeBSD diverges and produces systems that are functionally similar but logically very different.