Information about your files and directories is known as metadata. MediaIndexer uses a SQLite database for storing these properties. Since SQLite is bundled into PHP5, this makes it possible to not require any installation or configuration. When MediaIndexer is first run, it checks for the necessary database files and tables, and creates them automatically if they do not already exist.

The metadata stored in the database is completely maintained on-the-fly, and is transparent to your structure of your files. To identify files, it reads the first 1024 bytes of each of your files and creates a md5 checksum of this string. This hash is used as a unique key for identifying metadata in the database. This method allows you to move around your file structure as you like without having to keep the database synchronized. (this is new as of 0.7)

In short, administrative maintenance is not necessary. There are no cron scripts to run, etc.