Custom IOS, aka cIOS, are third-party IOS files that are installed on the wii. Most cIOS's are used for pirating. They are often made by using a base IOS with desirable features, such as USB support or Rockband microphone support and modified to install to a different slot such as 254 and then add extra features, such as restoring the trucha bug and adding piracy related functions.
Due to its heavy links with piracy, the word cIOS is generally avoided by most of the anti-piracy community, instead preferring more generic terms such as "patched IOS" when writing programs that require them.
With the discovery of the HW_AHBPROT register and integration of the related access flag into the Homebrew Channel's access permissions field, most homebrew should no longer depend on a modified IOS in order to do things which normally would require them. Thus, homebrew which requires custom IOS should be removed and replaced with less invasive, more modern alternatives.
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