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There are a variety of boot loaders for Linux, several of which are available in Funtoo. Configuring these boot loaders can be a challenge, so Funtoo provides a unified tool that generates appropriate configurations from a central configuration tool. That tool is Funtoo boot-update.

In addition to a unified configuration tool, Funtoo also makes newer versions of GNU GRUB available, with all of the improvements that come with that.

Funtoo also replaces Gentoo's init scripts with a snappier C-based Funtoo OpenRC.