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How do multisites have the ability to customize the look of the theme (menu color, style, etc.) without changing it for everyone else.

Where are these separate files stored?

  • Do you mean that the theme is customized on each site in a Multisite network, or that the theme is customized for each user on a specific site? If the former, have a look at the Customizer API. – Pat J Sep 12 '15 at 16:33
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Looking into the Theme Customizer API, it appears that theme modifications are stored as theme_mods which can be access using get_theme_mod( $mod_name ) or (if you want to grab them all) get_theme_mods().

Peeking into the source of get_theme_mods(), I see that the mods are stored in the site's options table as theme_mod_$mod_name. So the theme modifications are stored in the database, not in any files.

References

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You can create child themes to add modifications to the design of a specific website from your multisite network. These modifications are stored in the folder of your child theme.

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