Jet Pack erroneously deactivates plugins in other multi-site sites
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When you install JetPack in a subsite of a multi-site it deactivates plugins that are already installed that JetPack also provides. This is correct behaviour in a single site setup.
In a multi-site (3.6) JetPack deactivates the plugins in ALL sites on the multi-site. So for instance if you have Grunion contact form running in one subsite, activating JetPack in another subsite causes the unrelated subsite to end up with a deactivaed plugin.
The problem lies in class.jetpack-client-server.php lines 116 & 124 where deactivate_plugins( ) is called with a null second parameter which will de-activate network wide.
see
deactivate_plugins ( $plugins, $silent = false, $network_wide = null ) Parameters: (string|array) $plugins Single plugin or list of plugins to deactivate. (bool) $silent Prevent calling deactivation hooks. Default is false. (mixed) $network_wide Whether to deactivate the plugin for all sites in the network. A value of null (the default) will deactivate plugins for both the site and the network.
I think this is just a bug that can simply be fixed. Please let me know.
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