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I've created a multisite for a local charitable organization that contains five sub-clinics inside it. I have various plugins running (security, SEO, etc.) in the multisite activated "across the network".

I'd like to grant permissions for a user at this organization to check for updates every two days and apply any updates that come up. I don't necessarily want this user to have permissions to do anything else.

Is there a user level or a way to homebrew a user level that allows them to (a) log into the backend, (b) look for updates, and (c) update the multisite without giving them other authorial or editing permissions?

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The best way is to define a new role. An easy way to accomplish this is with the role scoper plugin. Otherwise you'll just have to write that plugin yourself manually.

Here is a basic example pulled from the Codex

$result = add_role(
    'basic_contributor',
    __( 'Basic Contributor' ),
    array(
        'read'         => true,  // true allows this capability
        'edit_posts'   => true,
        'delete_posts' => false, // Use false to explicitly deny
    )
);
if ( null !== $result ) {
    echo 'Yay! New role created!';
}
else {
    echo 'Oh... the basic_contributor role already exists.';
}

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